[R/bootstrap.R:5:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L5) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:6:75:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L6) *style:* **Trailing whitespace is superfluous.**
```r
#' @param SE_scored a \code{SummarizedExperiment} object with genes as the
                                                                          ^
```
[R/bootstrap.R:7:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L7) *style:* **Trailing whitespace is superfluous.**
```r
#' row features and signature scores in the \code{colData}. There should also
                                                                             ^
```
[R/bootstrap.R:9:73:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L9) *style:* **Trailing whitespace is superfluous.**
```r
#' @param annotationColName a character string giving the column name in
                                                                        ^
```
[R/bootstrap.R:11:60:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L11) *style:* **Trailing whitespace is superfluous.**
```r
#' @param SignatureColNames a vector of column names in the
                                                           ^
```
[R/bootstrap.R:13:75:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L13) *style:* **Trailing whitespace is superfluous.**
```r
#' @param num.boot integer. The number of times to bootstrap the data. The
                                                                          ^
```
[R/bootstrap.R:17:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L17) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:18:76:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L18) *style:* **Trailing whitespace is superfluous.**
```r
#' @return A list of length 3 returning a vector of p-values for a 2-sample
                                                                           ^
```
[R/bootstrap.R:19:81:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L19) *style:* **Trailing whitespace is superfluous.**
```r
#' t-test, bootstrapped AUC values, and an AUC value for using all scored values
                                                                                ^
```
[R/bootstrap.R:21:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L21) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:23:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L23) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:24:13:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L24) *style:* **Trailing whitespace is superfluous.**
```r
#' @examples
            ^
```
[R/bootstrap.R:27:71:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L27) *style:* **Trailing whitespace is superfluous.**
```r
#'  prof_indian <- runTBsigProfiler(TB_indian, useAssay = "logcounts",
                                                                      ^~
```
[R/bootstrap.R:34:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L34) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~
```
[R/bootstrap.R:35:74:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L35) *style:* **Trailing whitespace is superfluous.**
```r
bootstrapAUC <- function(SE_scored, annotationColName, signatureColNames,
                                                                         ^
```
[R/bootstrap.R:38:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L38) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:41:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L41) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:45:5:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L45) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(pb.show)  pb <- txtProgressBar(min = 0, max = total, style = 3)
    ^
```
[R/bootstrap.R:46:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L46) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:52:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L52) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/bootstrap.R:57:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L57) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/bootstrap.R:61:51:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L61) *style:* **Use TRUE instead of the symbol T.**
```r
      index <- sample(1:length(score), replace = T)
                                                 ~^
```
[R/bootstrap.R:69:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L69) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/bootstrap.R:74:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L74) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:81:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L81) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:82:80:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L82) *style:* **Trailing whitespace is superfluous.**
```r
#' This function collects the results of bootstrapping and t-tests for a scored
                                                                               ^
```
[R/bootstrap.R:83:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L83) *style:* **Trailing whitespace is superfluous.**
```r
#' gene expression dataset and presents them using a JavaScript table with an
                                                                             ^
```
[R/bootstrap.R:87:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L87) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:89:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L89) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:90:79:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L90) *style:* **Trailing whitespace is superfluous.**
```r
#' @return A JavaScript table with an R interface using the \code{DT} package.
                                                                              ^
```
[R/bootstrap.R:91:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L91) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:92:13:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L92) *style:* **Trailing whitespace is superfluous.**
```r
#' @examples
            ^
```
[R/bootstrap.R:95:71:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L95) *style:* **Trailing whitespace is superfluous.**
```r
#'  prof_indian <- runTBsigProfiler(TB_indian, useAssay = "logcounts",
                                                                      ^~
```
[R/bootstrap.R:99:67:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L99) *style:* **Trailing whitespace is superfluous.**
```r
#'  tableAUC(SE_scored = prof_indian, annotationColName = "label",
                                                                  ^
```
[R/bootstrap.R:101:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L101) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~
```
[R/bootstrap.R:102:70:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L102) *style:* **Trailing whitespace is superfluous.**
```r
tableAUC <- function(SE_scored, annotationColName, signatureColNames,
                                                                     ^
```
[R/bootstrap.R:105:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L105) *style:* **Trailing whitespace is superfluous.**
```r
  BS.Results <- bootstrapAUC(SE_scored, annotationColName, signatureColNames,
                                                                             ^
```
[R/bootstrap.R:110:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L110) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:112:63:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L112) *style:* **Trailing whitespace is superfluous.**
```r
  return(DT::datatable(cbind("Signatures" = signatureColNames,
                                                              ^
```
[R/bootstrap.R:113:59:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L113) *style:* **Trailing whitespace is superfluous.**
```r
                             "P-values" = round(pvals, 4),
                                                          ^
```
[R/bootstrap.R:114:79:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L114) *style:* **Trailing whitespace is superfluous.**
```r
                             "-10*Log(p-values)" = round(-10 * log(pvals), 4),
                                                                              ^
```
[R/bootstrap.R:115:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L115) *style:* **Trailing whitespace is superfluous.**
```r
                             "LowerAUC" = round(apply(aucs_boot, 2, quantile,
                                                                             ^
```
[R/bootstrap.R:116:72:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L116) *style:* **Trailing whitespace is superfluous.**
```r
                                                      probs = .05), 4),
                                                                       ^
```
[R/bootstrap.R:117:54:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L117) *style:* **Trailing whitespace is superfluous.**
```r
                             "AUCs" = round(aucs, 4),
                                                     ^
```
[R/bootstrap.R:118:40:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L118) *style:* **Put spaces around all infix operators.**
```r
                             "UpperAUC"= round(apply(aucs_boot, 2, quantile,
                                      ~^
```
[R/bootstrap.R:118:77:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L118) *style:* **Trailing whitespace is superfluous.**
```r
                             "UpperAUC"= round(apply(aucs_boot, 2, quantile,
                                                                            ^
```
[R/bootstrap.R:120:58:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L120) *style:* **Use TRUE instead of the symbol T.**
```r
                             )[order(aucs, decreasing = T),],
                                                        ~^
```
[R/bootstrap.R:120:60:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L120) *style:* **Commas should always have a space after.**
```r
                             )[order(aucs, decreasing = T),],
                                                           ^
```
[R/bootstrap.R:120:62:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L120) *style:* **Trailing whitespace is superfluous.**
```r
                             )[order(aucs, decreasing = T),],
                                                             ^
```
[R/bootstrap.R:121:50:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L121) *style:* **Use TRUE instead of the symbol T.**
```r
                       options = list(scrollX = T, pageLength = 10),
                                                ~^
```
[R/bootstrap.R:121:69:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L121) *style:* **Trailing whitespace is superfluous.**
```r
                       options = list(scrollX = T, pageLength = 10),
                                                                    ^
```
[R/bootstrap.R:122:36:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L122) *style:* **Use FALSE instead of the symbol F.**
```r
                       rownames = F))
                                  ~^
```
[R/bootstrap.R:126:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L126) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:127:71:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L127) *style:* **Trailing whitespace is superfluous.**
```r
#' Present the results of AUC bootstrapping for a collection of scored
                                                                      ^
```
[R/bootstrap.R:131:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L131) *style:* **Trailing whitespace is superfluous.**
```r
#' @param num.boot an integer indicating the number of times to bootstrap the
                                                                             ^
```
[R/bootstrap.R:133:79:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L133) *style:* **Trailing whitespace is superfluous.**
```r
#' @param cex.axis a number between 0 and 1 specifying the magnification to be
                                                                              ^
```
[R/bootstrap.R:134:75:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L134) *style:* **Trailing whitespace is superfluous.**
```r
#' used for axis annotation relative to the current setting of \code{cex}.
                                                                          ^
```
[R/bootstrap.R:135:80:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L135) *style:* **Trailing whitespace is superfluous.**
```r
#' @param cex a number between 0 and 1 giving the amount by which plotting text
                                                                               ^
```
[R/bootstrap.R:139:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L139) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:141:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L141) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:142:76:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L142) *style:* **Trailing whitespace is superfluous.**
```r
#' @return A plot with side-by-side boxplots of bootstrapped AUC values for
                                                                           ^
```
[R/bootstrap.R:144:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L144) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:145:13:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L145) *style:* **Trailing whitespace is superfluous.**
```r
#' @examples
            ^
```
[R/bootstrap.R:148:71:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L148) *style:* **Trailing whitespace is superfluous.**
```r
#'  prof_indian <- runTBsigProfiler(TB_indian, useAssay = "logcounts",
                                                                      ^~
```
[R/bootstrap.R:154:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L154) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~~~~~~~~~~
```
[R/bootstrap.R:155:77:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L155) *style:* **Trailing whitespace is superfluous.**
```r
compareBoxplots <- function(SE_scored, annotationColName, signatureColNames,
                                                                            ^
```
[R/bootstrap.R:159:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L159) *style:* **Trailing whitespace is superfluous.**
```r
  BS.Results <- bootstrapAUC(SE_scored, annotationColName, signatureColNames,
                                                                             ^
```
[R/bootstrap.R:170:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L170) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:174:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L174) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:176:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L176) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:178:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L178) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:179:13:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L179) *style:* **Trailing whitespace is superfluous.**
```r
#' @examples
            ^
```
[R/bootstrap.R:182:71:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L182) *style:* **Trailing whitespace is superfluous.**
```r
#'  prof_indian <- runTBsigProfiler(TB_indian, useAssay = "logcounts",
                                                                      ^~
```
[R/bootstrap.R:185:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L185) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bootstrap.R:189:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L189) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:194:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L194) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:239:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L239) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:247:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L247) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:253:60:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L253) *style:* **Trailing whitespace is superfluous.**
```r
    plot_n <- as.data.frame(cbind(FPR = round(pred$FPR, 4),
                                                           ^
```
[R/bootstrap.R:260:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L260) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:263:43:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L263) *style:* **Trailing whitespace is superfluous.**
```r
      "Empirical ROC curve")), size = 1) +
                                          ^
```
[R/bootstrap.R:264:53:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L264) *style:* **Trailing whitespace is superfluous.**
```r
    ggplot2::facet_wrap(~Signature, scales = 'free',
                                                    ^
```
[R/bootstrap.R:266:64:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L266) *style:* **Trailing whitespace is superfluous.**
```r
    ggplot2::geom_abline(ggplot2::aes(intercept = 0, slope = 1,
                                                               ^
```
[R/bootstrap.R:267:73:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L267) *style:* **Trailing whitespace is superfluous.**
```r
                                      col = choose_colors[2]), size = 1,
                                                                        ^
```
[R/bootstrap.R:271:36:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L271) *style:* **Trailing whitespace is superfluous.**
```r
    ggplot2::scale_color_manual("",
                                   ^
```
[R/bootstrap.R:275:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L275) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:280:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L280) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:283:62:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L283) *style:* **Trailing whitespace is superfluous.**
```r
#' in the ROC plots. The default is \code{c("cornflowerblue",
                                                             ^
```
[R/bootstrap.R:285:70:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L285) *style:* **Trailing whitespace is superfluous.**
```r
#' @param name a character string giving the title of the boxplot. If
                                                                     ^
```
[R/bootstrap.R:286:39:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L286) *style:* **Trailing whitespace is superfluous.**
```r
#' \code{NULL}, the plot title will be
                                      ^
```
[R/bootstrap.R:287:66:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L287) *style:* **Trailing whitespace is superfluous.**
```r
#' \code{"ROC plots for Gene Signatures, <ci.lev>\% Confidence"}.
                                                                 ^
```
[R/bootstrap.R:289:70:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L289) *style:* **Trailing whitespace is superfluous.**
```r
#' @param ci.lev a number between 0 and 1 giving the desired level of
                                                                     ^
```
[R/bootstrap.R:291:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L291) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:293:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L293) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:295:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L295) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:296:13:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L296) *style:* **Trailing whitespace is superfluous.**
```r
#' @examples
            ^
```
[R/bootstrap.R:299:71:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L299) *style:* **Trailing whitespace is superfluous.**
```r
#'  prof_indian <- runTBsigProfiler(TB_indian, useAssay = "logcounts",
                                                                      ^~
```
[R/bootstrap.R:302:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L302) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bootstrap.R:306:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L306) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:309:68:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L309) *style:* **Trailing whitespace is superfluous.**
```r
                                choose_colors = c("cornflowerblue",
                                                                   ^
```
[R/bootstrap.R:313:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L313) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:358:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L358) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:366:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L366) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:369:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L369) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:374:7:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L374) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(any(is.nan(this.conf$UpperTPR))) {
      ^
```
[R/bootstrap.R:377:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L377) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/bootstrap.R:378:65:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L378) *style:* **Trailing whitespace is superfluous.**
```r
    plot_n <- as.data.frame(cbind(FPR = round(this.conf$FPR, 4),
                                                                ^
```
[R/bootstrap.R:379:65:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L379) *style:* **Trailing whitespace is superfluous.**
```r
                                  TPR = round(this.conf$TPR, 4),
                                                                ^
```
[R/bootstrap.R:385:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L385) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:387:13:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L387) *style:* **Commas should always have a space after.**
```r
  plot_dat[,1:4] <- as.data.frame(apply(plot_dat[,1:4], 2, as.numeric))
            ^
```
[R/bootstrap.R:387:51:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L387) *style:* **Commas should always have a space after.**
```r
  plot_dat[,1:4] <- as.data.frame(apply(plot_dat[,1:4], 2, as.numeric))
                                                  ^
```
[R/bootstrap.R:388:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L388) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:389:5:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L389) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.null(name)) name <- paste("ROC plots for Gene Signatures, ", ci.lev*100,
    ^
```
[R/bootstrap.R:389:76:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L389) *style:* **Put spaces around all infix operators.**
```r
  if(is.null(name)) name <- paste("ROC plots for Gene Signatures, ", ci.lev*100,
                                                                          ~^~
```
[R/bootstrap.R:389:81:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L389) *style:* **Trailing whitespace is superfluous.**
```r
  if(is.null(name)) name <- paste("ROC plots for Gene Signatures, ", ci.lev*100,
                                                                                ^
```
[R/bootstrap.R:391:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L391) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:393:72:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L393) *style:* **Trailing whitespace is superfluous.**
```r
    ggplot2::geom_ribbon(ggplot2::aes(ymin = LowerTPR, ymax = UpperTPR,
                                                                       ^
```
[R/bootstrap.R:394:69:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L394) *style:* **Trailing whitespace is superfluous.**
```r
                                      fill = "Confidence Interval"),
                                                                    ^
```
[R/bootstrap.R:396:60:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L396) *style:* **Trailing whitespace is superfluous.**
```r
    ggplot2::geom_line(ggplot2::aes(x = FPR, y = TPR, col =
                                                           ^
```
[R/bootstrap.R:397:74:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L397) *style:* **Trailing whitespace is superfluous.**
```r
                                      "Empirical ROC curve"), size = 1) +
                                                                         ^
```
[R/bootstrap.R:398:53:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L398) *style:* **Trailing whitespace is superfluous.**
```r
    ggplot2::facet_wrap(~Signature, scales = 'free',
                                                    ^
```
[R/bootstrap.R:400:64:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L400) *style:* **Trailing whitespace is superfluous.**
```r
    ggplot2::geom_abline(ggplot2::aes(intercept = 0, slope = 1,
                                                               ^
```
[R/bootstrap.R:401:73:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L401) *style:* **Trailing whitespace is superfluous.**
```r
                                      col = choose_colors[2]), size = 1,
                                                                        ^
```
[R/bootstrap.R:403:36:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L403) *style:* **Trailing whitespace is superfluous.**
```r
    ggplot2::scale_color_manual("",
                                   ^
```
[R/bootstrap.R:406:35:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L406) *style:* **Trailing whitespace is superfluous.**
```r
    ggplot2::scale_fill_manual("",
                                  ^
```
[R/bootstrap.R:412:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L412) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:417:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L417) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:418:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L418) *style:* **Trailing whitespace is superfluous.**
```r
#' Given an input of a Summarized Experiment with a counts or CPM assay, This
                                                                             ^
```
[R/bootstrap.R:419:74:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L419) *style:* **Trailing whitespace is superfluous.**
```r
#' function creates additional assays for a gene expression count dataset
                                                                         ^
```
[R/bootstrap.R:421:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L421) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:430:63:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L430) *style:* **Trailing whitespace is superfluous.**
```r
#' of whichever assay is specified in \code{"output_name"}. If
                                                              ^
```
[R/bootstrap.R:432:40:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L432) *style:* **Trailing whitespace is superfluous.**
```r
#' be created. Default is \code{FALSE}.
                                       ^
```
[R/bootstrap.R:433:67:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L433) *style:* **Trailing whitespace is superfluous.**
```r
#' @param counts_to_CPM logical. This argument only applies if the
                                                                  ^
```
[R/bootstrap.R:435:80:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L435) *style:* **Trailing whitespace is superfluous.**
```r
#' will include a normalized CPM assay. If \code{counts_to_CPM = TRUE} as well,
                                                                               ^
```
[R/bootstrap.R:436:70:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L436) *style:* **Trailing whitespace is superfluous.**
```r
#' then a log CPM assay will also be created. Default is \code{TRUE}.
                                                                     ^~
```
[R/bootstrap.R:437:79:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L437) *style:* **Trailing whitespace is superfluous.**
```r
#' @param  prior.counts an integer specifying the average count to be added to
                                                                              ^
```
[R/bootstrap.R:438:66:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L438) *style:* **Trailing whitespace is superfluous.**
```r
#' each observation to avoid taking the log of zero. Used only if
                                                                 ^
```
[R/bootstrap.R:440:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L440) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:441:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L441) *style:* **Trailing whitespace is superfluous.**
```r
#' @return This function returns a \code{SummarizedExperiment} object with up
                                                                             ^
```
[R/bootstrap.R:445:60:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L445) *style:* **Trailing whitespace is superfluous.**
```r
#' \item{log_<output_name>}{Log of original inputted assay.
                                                           ^
```
[R/bootstrap.R:447:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L447) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:448:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L448) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:450:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L450) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:452:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L452) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:453:13:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L453) *style:* **Trailing whitespace is superfluous.**
```r
#' @examples
            ^
```
[R/bootstrap.R:458:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L458) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:462:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L462) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:466:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L466) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bootstrap.R:471:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L471) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:473:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L473) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:477:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L477) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:483:4:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L483) *style:* **Trailing whitespace is superfluous.**
```r
  }
   ^
```
[R/bootstrap.R:484:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L484) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:487:72:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L487) *style:* **Trailing whitespace is superfluous.**
```r
      SE_obj, paste("log", output_name, sep = "_")) <- log(assay_main +
                                                                       ^
```
[R/bootstrap.R:489:4:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L489) *style:* **Trailing whitespace is superfluous.**
```r
  }
   ^
```
[R/bootstrap.R:490:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L490) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bootstrap.R:496:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/bootstrap.R#L496) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/data.R:3:80:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/data.R#L3) *style:* **Trailing whitespace is superfluous.**
```r
#' A set of 34 Tuberculosis gene signatures from various publications. This set
                                                                               ^
```
[R/data.R:4:80:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/data.R#L4) *style:* **Trailing whitespace is superfluous.**
```r
#' of signatures uses gene symbols. Attempts have been made to use updated gene
                                                                               ^
```
[R/data.R:5:77:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/data.R#L5) *style:* **Trailing whitespace is superfluous.**
```r
#' symbols and remove symbols that did not match the most recent annotation.
                                                                            ^
```
[R/data.R:6:80:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/data.R#L6) *style:* **Trailing whitespace is superfluous.**
```r
#' Additional sets for Entrez IDs and Ensembl IDs are forthcoming. The assigned
                                                                               ^
```
[R/data.R:7:75:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/data.R#L7) *style:* **Trailing whitespace is superfluous.**
```r
#' signature name ends with the number of genes in the original signature.
                                                                          ^
```
[R/data.R:9:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/data.R#L9) *style:* **Trailing whitespace is superfluous.**
```r
#' whereas others are negative identifiers. This should be taken into account
                                                                             ^
```
[R/data.R:52:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/data.R#L52) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~
```
[R/data.R:61:113:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/data.R#L61) *style:* **Trailing whitespace is superfluous.**
```r
#' An example dataset containing the gene expression and metadata in a SummarizedExperiment object for an Indian
                                                                                ^
```
[R/data.R:63:83:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/data.R#L63) *style:* **Trailing whitespace is superfluous.**
```r
#' and can be accessed via \code{TB_indian$label}. The SummarizedExperiment object
                                                                                ^
```
[R/data.R:79:89:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/data.R#L79) *style:* **Trailing whitespace is superfluous.**
```r
#' Samples with both TB and HIV contamination are marked as \code{tb_hiv}, while samples
                                                                                ^
```
[R/evaluate.R:2:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L2) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/evaluate.R:3:76:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L3) *style:* **Trailing whitespace is superfluous.**
```r
#' @param inputData a \code{data.frame} or \code{matrix} of gene expression
                                                                           ^
```
[R/evaluate.R:5:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L5) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/evaluate.R:10:13:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L10) *style:* **Trailing whitespace is superfluous.**
```r
#' @examples
            ^
```
[R/evaluate.R:26:72:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L26) *style:* **Trailing whitespace is superfluous.**
```r
#' @param targetVec a binary vector of the response variable. Should be
                                                                       ^
```
[R/evaluate.R:28:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L28) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/evaluate.R:29:44:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L29) *style:* **Trailing whitespace is superfluous.**
```r
#' @return A list of length 3 with elements
                                           ^
```
[R/evaluate.R:30:49:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L30) *style:* **Trailing whitespace is superfluous.**
```r
#' \item{auc}{The AUC from the LOOCV procedure.}
                                                ^
```
[R/evaluate.R:31:77:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L31) *style:* **Trailing whitespace is superfluous.**
```r
#' \item{byClass}{A vector containing the sensitivity, specificity, positive
                                                                            ^
```
[R/evaluate.R:32:71:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L32) *style:* **Trailing whitespace is superfluous.**
```r
#' predictive value, negative predictive value, precision, recall, F1,
                                                                      ^
```
[R/evaluate.R:49:65:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L49) *style:* **Trailing whitespace is superfluous.**
```r
    fit <- suppressWarnings(glmnet::glmnet(train, targetVec[-j],
                                                                ^
```
[R/evaluate.R:62:62:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L62) *style:* **Trailing whitespace is superfluous.**
```r
    caret::confusionMatrix(as.factor(testPredictionClassVec),
                                                             ^
```
[R/evaluate.R:75:72:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L75) *style:* **Trailing whitespace is superfluous.**
```r
#' @param targetVec a binary vector of the response variable. Should be
                                                                       ^
```
[R/evaluate.R:79:78:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L79) *style:* **Trailing whitespace is superfluous.**
```r
#' @return A list of length 2 with elements \item{auc}{A vector the length of
                                                                             ^
```
[R/evaluate.R:84:71:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L84) *style:* **Trailing whitespace is superfluous.**
```r
#' detection rate, detection prevalence and balanced accuracy for that
                                                                      ^
```
[R/evaluate.R:115:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L115) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/evaluate.R:118:74:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L118) *style:* **Trailing whitespace is superfluous.**
```r
#' with logistic regression to allow for numeric and graphical comparison
                                                                         ^
```
[R/evaluate.R:122:75:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L122) *style:* **Trailing whitespace is superfluous.**
```r
#' @param target.vec.num a numeric binary vector of the response variable.
                                                                          ^
```
[R/evaluate.R:124:71:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L124) *style:* **Trailing whitespace is superfluous.**
```r
#' @param signature.list a \code{list} of signatures to run with their
                                                                      ^
```
[R/evaluate.R:125:84:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L125) *style:* **Trailing whitespace is superfluous.**
```r
#' associated genes. This list should be in the same format as \code{TBsignatures},
                                                                                ^
```
[R/evaluate.R:126:81:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L126) *style:* **Trailing whitespace is superfluous.**
```r
#' included in the TBSignatureProfiler package. If \code{signature.list = NULL},
                                                                                ^
```
[R/evaluate.R:127:80:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L127) *style:* **Trailing whitespace is superfluous.**
```r
#' the default set of signatures \code{TBsignatures} list is used. For details,
                                                                               ^
```
[R/evaluate.R:131:70:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L131) *style:* **Trailing whitespace is superfluous.**
```r
#' If \code{signature.name.vec = NULL}, the default set of signatures
                                                                     ^
```
[R/evaluate.R:134:70:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L134) *style:* **Trailing whitespace is superfluous.**
```r
#' @param pb.show logical. If \code{TRUE} then a progress bar for the
                                                                     ^
```
[R/evaluate.R:135:71:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L135) *style:* **Trailing whitespace is superfluous.**
```r
#' bootstrapping procedure will be displayed as output. The default is
                                                                      ^
```
[R/evaluate.R:137:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L137) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/evaluate.R:154:60:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L154) *style:* **Trailing whitespace is superfluous.**
```r
SignatureQuantitative <- function(df.input, target.vec.num,
                                                           ^
```
[R/evaluate.R:156:61:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L156) *style:* **Trailing whitespace is superfluous.**
```r
                                  signature.name.vec = NULL,
                                                            ^
```
[R/evaluate.R:159:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L159) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/evaluate.R:172:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L172) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/evaluate.R:177:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L177) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/evaluate.R:183:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L183) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/evaluate.R:192:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L192) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/evaluate.R:199:65:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L199) *style:* **Trailing whitespace is superfluous.**
```r
    result <- LOOAUC_simple_multiple_noplot_one_df(df.list[[i]],
                                                                ^
```
[R/evaluate.R:204:19:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L204) *style:* **Put spaces around all infix operators.**
```r
    st.error <- (1/(num.boot-1))*sum(auc.result[[i]] - mean(auc.result[[i]]))
                 ~^~
```
[R/evaluate.R:204:20:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L204) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    st.error <- (1/(num.boot-1))*sum(auc.result[[i]] - mean(auc.result[[i]]))
                   ^
```
[R/evaluate.R:204:29:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L204) *style:* **Put spaces around all infix operators.**
```r
    st.error <- (1/(num.boot-1))*sum(auc.result[[i]] - mean(auc.result[[i]]))
                           ~^~
```
[R/evaluate.R:204:33:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L204) *style:* **Put spaces around all infix operators.**
```r
    st.error <- (1/(num.boot-1))*sum(auc.result[[i]] - mean(auc.result[[i]]))
                               ~^~
```
[R/evaluate.R:213:40:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L213) *style:* **Trailing whitespace is superfluous.**
```r
    st.error2 <- (1 / (num.boot - 1)) *
                                       ^
```
[R/evaluate.R:214:46:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L214) *style:* **Trailing whitespace is superfluous.**
```r
      sum(boot.output.list[[2]]$Sensitivity -
                                             ^
```
[R/evaluate.R:215:53:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L215) *style:* **Trailing whitespace is superfluous.**
```r
            mean(boot.output.list[[2]]$Sensitivity))
                                                    ^
```
[R/evaluate.R:222:40:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L222) *style:* **Trailing whitespace is superfluous.**
```r
    st.error3 <- (1 / (num.boot - 1)) *
                                       ^
```
[R/evaluate.R:223:46:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L223) *style:* **Trailing whitespace is superfluous.**
```r
      sum(boot.output.list[[2]]$Specificity -
                                             ^
```
[R/evaluate.R:224:53:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L224) *style:* **Trailing whitespace is superfluous.**
```r
            mean(boot.output.list[[2]]$Specificity))
                                                    ^
```
[R/evaluate.R:230:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L230) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/evaluate.R:242:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L242) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/evaluate.R:261:1:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/evaluate.R#L261) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/plot.R:2:3:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/plot.R#L2) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/plot.R:4:66:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/plot.R#L4) *style:* **Trailing whitespace is superfluous.**
```r
#' and returns a ComplexHeatmap plot for for visual comparison of
                                                                 ^
```
[R/plot.R:7:75:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/plot.R#L7) *style:* **Trailing whitespace is superfluous.**
```r
#' @param inputData an input data object. It should either be of the class
                                                                          ^
```
[R/plot.R:8:75:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/plot.R#L8) *style:* **Trailing whitespace is superfluous.**
```r
#' \code{SummarizedExperiment} and contain the profiled signature data and
                                                                          ^
```
[R/plot.R:9:81:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/plot.R#L9) *style:* **Trailing whitespace is superfluous.**
```r
#' annotation data as columns in the colData, or alternatively be of the classes
                                                                                ^
```
[R/plot.R:10:81:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/plot.R#L10) *style:* **Trailing whitespace is superfluous.**
```r
#' \code{data.frame} or \code{matrix} and contain only the gene expression data.
                                                                                ^
```
[R/plot.R:12:76:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/plot.R#L12) *style:* **Trailing whitespace is superfluous.**
```r
#' @param annotationData a \code{data.frame} or \code{matrix} of annotation
                                                                           ^
```
[R/plot.R:15:74:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/plot.R#L15) *style:* **Trailing whitespace is superfluous.**
```r
#' @param name a character string with the plot title of the heatmap. The
                                                                         ^
```
[R/plot.R:17:80:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/plot.R#L17) *style:* **Trailing whitespace is superfluous.**
```r
#' @param signatureColNames a vector of the column names in \code{colData} that
                                                                               ^
```
[R/plot.R:18:70:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/plot.R#L18) *style:* **Trailing whitespace is superfluous.**
```r
#' contain the signature data. Only required if \code{inputData} is a
                                                                     ^
```
[R/plot.R:20:81:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/plot.R#L20) *style:* **Trailing whitespace is superfluous.**
```r
#' @param annotationColNames a vector of the column names in \code{colData} that
                                                                                ^
```
[R/plot.R:21:71:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/plot.R#L21) *style:* **Trailing whitespace is superfluous.**
```r
#' contain the annotation data. Only required if \code{inputData} is a
                                                                      ^
```
[R/plot.R:23:94:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/plot.R#L23) *style:* **Trailing whitespace is superfluous.**
```r
#' @param colList a named \code{list} of named vectors specifying custom color information to
                                                                                ^
```
[R/plot.R:26:63:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/plot.R#L26) *style:* **Trailing whitespace is superfluous.**
```r
#' correspond exactly with the name of each annotation column.
                                                              ^
```
[R/plot.R:27:70:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/plot.R#L27) *style:* **Trailing whitespace is superfluous.**
```r
#' The colors in the vector elements should be named according to the
                                                                     ^
```
[R/plot.R:31:59:](https://github.com/Aubreyodom/TBSignatureProfiler/blob/5762647c88e130d4d50a5ad8d1b13af7dcbca9e2/R/plot.R#L31) *style:* **Trailing whitespace is superfluous.**
```r
#' By default, \code{ColorBrewer} color sets will be used.
                                                          ^
```


Successfully aliased the URL <https://isaacbythewoodcom-yojiku6le.now.sh> to the following aliases:

* https://isaacbythewood.com
* https://www.isaacbythewood.com
* https://isaacbythewoodcom.overshard.now.sh
* https://isaacbythewoodcom-git-master.overshard.now.sh


Fixes #25


Successfully aliased the URL <https://my-port-folio-kic1sp93s.now.sh> to the following alias:

* https://my-port-folio-git-master.alaami.now.sh


Een zin beginnen met `En`?


merged branch 2nd line


add-diagnostic-script (jasondegraw) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-IntegrationCoverage-Debug: OK (667 of 667 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-68.45%25-green.png)


This may be an opportunity to create a `QueryFactory` class. We haven't talked about this much, but you generally want to separate your model code from your view code.

You can think of what happens in `StudentInboxFragment.java` as all view-related, and how this query is built is sort of separate. If you got this query like:

```java
final ParseQuery<Question> messageQuery = QueryFactory.inboxedQuestions();
messageQuery.findInBackground(new FindCallback<Question>() {
    ...
}
```

Just like we talked about in person, we can also namespace this by adding nested classes. So we can do `QueryFactory.inbox.getInboxMessages()`, or whatever 👍🏼


It should be 4.10.2 as thats what the other branches use.


VS 2019,  lines 49 and 51:
Warning	C4244	 '=': conversion from 'CryptoPP::sword64' to 'CryptoPP::word32', possible loss of data


super eres bienvenido


nnn


![](https://github.trello.services/images/mini-trello-icon.png) [add doc templates](https://trello.com/c/1BQLkbM4/51-add-doc-templates)


![](https://github.trello.services/images/mini-trello-icon.png) [add doc searching](https://trello.com/c/0XzyM3Fs/52-add-doc-searching)


![](https://github.trello.services/images/mini-trello-icon.png) [add doc searching and nav](https://trello.com/c/0XzyM3Fs/52-add-doc-searching-and-nav)


![](https://github.trello.services/images/mini-trello-icon.png) [add toc for each file in docs](https://trello.com/c/evKH7X95/53-add-toc-for-each-file-in-docs)


Stockcam


Added readme-edits line


@chemiker Sieht gut aus. Für Variablen in HTML Attributen ggf. [esc_attr](http://developer.wordpress.org/reference/functions/esc_attr/) verwenden, das ist explizit dafür da.


It's sad that the commit log doesn't point out the details why this commit is needed. I invested quite some time to debug the problem and (IMHO) described it in enough detail that someone stumbling over said commit is able to easily understand it. I can accept that you chose a different fix than I suggested, but at least pointing to the original discussion would have been nice.


Hmm, this is different from the [Python SDK PR](https://github.com/open-telemetry/opentelemetry-python/pull/58/files), which affects the ordering (by promoting the key to the newest). Which one is the intended behavior?


Do we ever use `hideModal`? I believe the modal will automatically close if you click the 'x' button.


Note for future reference:
The reason alt method is broken seems to be that it doesn't want to sqlite3_step() at all, it calls the callback, hits the while loop and instantly returns... o0


If this is in reference to citra. This is because citra is including dynarmic before fmt in its CMakeLists via add_subdirectory. This works fine with yuzu, which also defines `DYNARMIC_NO_BUNDLED_FMT`.


ok


add-diagnostic-script (jasondegraw) - Win64-Windows-10-VisualStudio-16: OK (2452 of 2452 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png)


Deployment failed with the following error:

~~~
Your `package.json` file is missing a `build` property inside the `script` property.
~~~


Successfully aliased the URL <https://babangsundcom-4m0u0itun.now.sh> to the following aliases:

* https://babangsund.com
* https://babangsundcom.babangsund.now.sh
* https://babangsundcom-git-master.babangsund.now.sh


1) Проверяем равенство объектов по ссылки с помощью знака равенства, если две ссылки ссылаются на одну ячейку памяти, соответственно это один и тот же объект, который мы создали в куче.


I don't trust this commit, changes have been requested multiple times upstream but it was never merged for a reason or another. Remove it, then pr it separately, we can't consider merging it until properly testing various use cases.


@JeremieHornus added the OS/2 code page check source that I used across Windows/macOS system fonts here


2) Проверяем сигнатуру классов, если название классов, которые создали объекты разные, то объекты являются
разные.


Failed to alias the deployment: Deployment not found.

[Click here](https://zeit.co/github/deployment?deploymentId=dpl_8FtFS1MH34vQJQh1NVMFPFdCKMJg) to access the non-aliased deployment.


Привидение типов класса User.


Hello. Please made "scanline effect" optionale ON / OFF. URL params option &scanline=true or false


Stock-cam


### federico me tenes re podrido


Failed to alias the deployment: Deployment not found.

[Click here](https://zeit.co/github/deployment?deploymentId=dpl_8CcBWDk1RTUb6D1abYvpDpsdW9AA) to access the non-aliased deployment.


Sure thing @kholk! However, it did successfully manually built kernels for yoshino and succeeded when using our build-kernels-gcc.sh in the ROM too for all devices.


Another nice change


Hoo boy. It's not just graphics that changed.

- Adds a new color (pink) for contact point when not touching the floor
- Makes `FLOOR_Z` a member of both `core::` and `graphics::`
- Switches to RMS color blending a la minutephysics (shrug)
- Adds contact point guessing methods for entities
- Automatically tries again with new guesses if a PATH step fails
- Adds new list of "visual only" entities to the simulation class (for previews, etc)
- Adds option to log calculation time when simulating (previously tied to logging verbose-ish calculation output)
- Consolidates `addSteps()` logic into one method (and into a lambda actually)
- Changes/overloads `Entity::renderShadow()`; one takes a "reference point" and shadow size, and another is lower-level by taking a shadow center, radius, and center alpha; last is the virtual one that's unique for each shape
- Actually renders two slightly different overlapping shadows for entities in an attempt to reduce the optical-illusiony bright ring effect (fade out more smoothly toward the edges of the shadow)
- Changes shadow rendering to take entity orientation into account
- Moves `Simulation` shadow rendering to its own method
- Changes render code to stop shadow Z-fighting (by adding more draw calls with depth stuff on/off; however this has the effect of making the floor appear opaque when looking from above which ig is acceptable)
- Adds methods to `Renderer` to enable/disable depth testing and depth buffer writing
- Adds optional parameters to `Renderer::renderAndClearAll()` to specify whether to use depth
- Minor GUI improvements (tooltips etc)
- Adds caching to `Entity::containsPoint()` and `Entity::to****Frame()`
- Adds utility method `Renderer::renderMarkerDot()`
- Changes `Box` to use 3 size fields instead of 6 (`VisualBox` still uses 6)
- Adds a close button to entity GUIs
- Adds a close button to the ImGui demo window
- Removes the legacy `Window::directRender()` methods
- Makes `Window::GuiOverlay` methods not virtual. Why would they need to be virtual?
- Gives `VisualCylinder` and `VisualSphere` more nodes to smooth their appearance
- `SOLID_COLOR` visual entities no longer run color mixing calculations

Note: RMS color mixing seems to make `VisualSphere` look weird, especially at the poles. Lol rip


Successfully aliased the URL <https://node-fd-nynsdmbzz.now.sh> to the following aliases:

* https://dev.biffy.nl
* https://node-fd.willemliu.now.sh
* https://node-fd-git-master.willemliu.now.sh


Successfully aliased the URL <https://videolistapi-cbvgy0exc.now.sh> to the following aliases:

* https://video-list-api.ljavierrodriguez.now.sh
* https://video-list-api-git-master.ljavierrodriguez.now.sh


Successfully aliased the URL <https://nextjs12-vx4oz3m88.now.sh> to the following aliases:

* https://nextjs12.gridml.now.sh
* https://nextjs12-git-master.gridml.now.sh


To clean this up slightly: I think it's fine to have separate functions for `goToCalendar` and `goToData`. But let's just have a single `redirect` state variable (we can call it `redirectTo`).
```
goToCalendar = () => {
    this.setState({
        redirectTo: '/calendar',
    });
};
goToData = () => {
    this.setState({
        redirectTo: '/data',
    });
};
```

Then we can just have a single rendering function:
```
render = () => {
    return <Redirect to={this.state.redirectTo} />
};
```


>
>
> having
>
> ```
> #define EXTRUDER_0_AUTO_FAN_PIN 255
> ```
>
> in `Configuration_adv.h` should be good enough...
>
making this change  to fan_pin 255, I get error compiling 'DIO 255_DDR' was not declared in this scope


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* https://nextjs13.lucleray.now.sh
* https://nextjs13-git-master.lucleray.now.sh


Проверяем равенство полей, с учетом бизнес - логике, если содержание полей двух объектов одинаковое, то
соответственно это два одинаковые объекта.
В противном случае вернет false.


This annotation also accepts the alternative form "namespace/secretName", in which case the ConfigMap lookup is performed in the referenced namespace instead of the Ingress namespace.


nvm.sh


Successfully aliased the URL <https://nextjs14-4ro36dqzx.now.sh> to the following aliases:

* https://nextjs14.gridml.now.sh
* https://nextjs14-git-master.gridml.now.sh


Рассказать и продемонстрировать как переопределяют метод equals.


0.4.0 was released yesterday - https://github.com/census-instrumentation/opencensus-cpp/releases/tag/v0.4.0. Can we switch from a commit to the release?


closes #3


Well done bro. invite me to your discord if you have it still running. I also have mine here: https://github.com/isaac-diaby/CGB-Core


Successfully aliased the URL <https://destiny-report-cfjluqwr1.now.sh> to the following aliases:

* https://destiny.report
* https://destiny-report.sarkurd.now.sh
* https://destiny-report-git-master.sarkurd.now.sh


Perhaps "File path where the office-addin-telemetry config data is stored.  By default, the config data is stored in %USERPROFILE%\officeAddinTelemetry.json"