[R/inference-chisq_statistic.R:44:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-chisq_statistic.R#L44) *style:* **lines should not be more than 80 characters.**
```r
  if (length(maha)  != nrow(obj)) stop("length(mahalanobis distance) != nrow(obj)")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-diffuse.R:57:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L57) *style:* **lines should not be more than 80 characters.**
```r
                                        path=NULL, graph=NULL, r=0.5, node.start.count=25,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-diffuse.R:58:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L58) *style:* **lines should not be more than 80 characters.**
```r
                                        search.depth=5, delete.nodes.on.degree=1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-diffuse.R:62:19:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L62) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::select(GeneSymbol, abs(Effect))
                  ^~~~~~~~~~
```
[R/inference-diffuse.R:68:21:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L68) *style:* **Variable and function names should be all lowercase.**
```r
      dplyr::filter(GeneSymbol %in% hits$GeneSymbol) %>%
                    ^~~~~~~~~~
```
[R/inference-diffuse.R:68:42:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L68) *style:* **Variable and function names should be all lowercase.**
```r
      dplyr::filter(GeneSymbol %in% hits$GeneSymbol) %>%
                                         ^~~~~~~~~~
```
[R/inference-diffuse.R:69:22:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L69) *style:* **Variable and function names should be all lowercase.**
```r
      dplyr::select(-MeanBootstrap, -Pval, -FDR)
                     ^~~~~~~~~~~~~
```
[R/inference-diffuse.R:86:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L86) *style:* **lines should not be more than 80 characters.**
```r
                               path=NULL, graph=NULL, r=0.5, node.start.count=25,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-diffuse.R:93:21:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L93) *style:* **Variable and function names should be all lowercase.**
```r
      dplyr::select(GeneSymbol, Readout) %>%
                    ^~~~~~~~~~
```
[R/inference-diffuse.R:99:21:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L99) *style:* **Variable and function names should be all lowercase.**
```r
      dplyr::select(GeneSymbol, MeanEffect) %>%
                    ^~~~~~~~~~
```
[R/inference-diffuse.R:99:33:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L99) *style:* **Variable and function names should be all lowercase.**
```r
      dplyr::select(GeneSymbol, MeanEffect) %>%
                                ^~~~~~~~~~
```
[R/inference-diffuse.R:100:28:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L100) *style:* **Variable and function names should be all lowercase.**
```r
      dplyr::rename(Effect=MeanEffect)
                           ^~~~~~~~~~
```
[R/inference-diffuse.R:104:35:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L104) *style:* **Variable and function names should be all lowercase.**
```r
    hits <- obj %>% dplyr::select(GeneSymbol, Effect)
                                  ^~~~~~~~~~
```
[R/inference-diffuse.R:132:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L132) *style:* **lines should not be more than 80 characters.**
```r
         "neighbors"= .knn(hits, bootstrap.hits, adjm, node.start.count, search.depth, graph),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-diffuse.R:153:44:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L153) *style:* **Variable and function names should be all lowercase.**
```r
  li  <- list(diffusion=dplyr::select(res, GeneSymbol, Effect, DiffusionEffect),
                                           ^~~~~~~~~~
```
[R/inference-diffuse.R:153:64:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L153) *style:* **Variable and function names should be all lowercase.**
```r
  li  <- list(diffusion=dplyr::select(res, GeneSymbol, Effect, DiffusionEffect),
                                                               ^~~~~~~~~~~~~~~
```
[R/inference-diffuse.R:167:22:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L167) *style:* **Variable and function names should be all lowercase.**
```r
  diffuse.data$frame$DiffusionEffect <- mrw
                     ^~~~~~~~~~~~~~~
```
[R/inference-diffuse.R:189:58:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L189) *style:* **Variable and function names should be all lowercase.**
```r
  boot.g <- tidyr::gather(bootstrap.hits, Boot, Effect, -GeneSymbol) %>%
                                                         ^~~~~~~~~~
```
[R/inference-diffuse.R:201:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L201) *style:* **lines should not be more than 80 characters.**
```r
  # -> calculate means -> calculate alphas -> calculate variance -> calculate alpha_0
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-diffuse.R:202:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L202) *style:* **lines should not be more than 80 characters.**
```r
  flat.dat <- do.call("rbind", lapply(li, function(e) e)) %>% dplyr::select(-Effect)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-diffuse.R:204:21:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L204) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::group_by(GeneSymbol) %>%
                    ^~~~~~~~~~
```
[R/inference-diffuse.R:205:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L205) *style:* **lines should not be more than 80 characters.**
```r
    dplyr::summarise(MeanBootstrapDiffusionEffect=mean(DiffusionEffect, na.rm=T)) %>%
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-diffuse.R:205:56:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L205) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::summarise(MeanBootstrapDiffusionEffect=mean(DiffusionEffect, na.rm=T)) %>%
                                                       ^~~~~~~~~~~~~~~
```
[R/inference-diffuse.R:208:57:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L208) *style:* **Variable and function names should be all lowercase.**
```r
                          tidyr::spread(flat.dat, boot, DiffusionEffect),
                                                        ^~~~~~~~~~~~~~~
```
[R/inference-diffuse.R:216:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L216) *style:* **lines should not be more than 80 characters.**
```r
.knn <- function(hits, bootstrap.hits, adjm, node.start.count, search.depth, graph)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-diffuse.R:226:56:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L226) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::filter(Idx %in% as.integer(names(neighs))))$GeneSymbol
                                                       ^~~~~~~~~~
```
[R/inference-diffuse.R:230:21:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L230) *style:* **Variable and function names should be all lowercase.**
```r
      dplyr::select(GeneSymbol, Effect)}
                    ^~~~~~~~~~
```
[R/inference-diffuse.R:239:49:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-diffuse.R#L239) *style:* **Variable and function names should be all lowercase.**
```r
  genes.found <- dplyr::select(flat.dat, Start, GeneSymbol) %>%
                                                ^~~~~~~~~~
```
[R/inference-gesper.R:59:47:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-gesper.R#L59) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::filter(obj, !is.na(Entrez), !is.na(siRNAIDs)) %>%
                                              ^~~~~~~~
```
[R/inference-gesper.R:65:33:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-gesper.R#L65) *style:* **Variable and function names should be all lowercase.**
```r
    res <- dplyr::group_by(res, GeneSymbol) %>%
                                ^~~~~~~~~~
```
[R/inference-gesper.R:72:10:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-gesper.R#L72) *style:* **Variable and function names should be all lowercase.**
```r
  res <- .gespeR(res, path)
         ^~~~~~~
```
[R/inference-gesper.R:79:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-gesper.R#L79) *style:* **Variable and function names should be all lowercase.**
```r
.gespeR <- function(obj, path)
^~~~~~~
```
[R/inference-gesper.R:83:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-gesper.R#L83) *style:* **lines should not be more than 80 characters.**
```r
  # init the matrices so that all entrez id that are not in both matrices are discarded
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-gesper.R:90:61:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-gesper.R#L90) *style:* **Variable and function names should be all lowercase.**
```r
                               ids=as.character(pheno.frame$siRNAIDs),
                                                            ^~~~~~~~
```
[R/inference-gesper.R:104:45:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-gesper.R#L104) *style:* **Variable and function names should be all lowercase.**
```r
                         dplyr::select(obj, GeneSymbol, Entrez) %>% unique,
                                            ^~~~~~~~~~
```
[R/inference-gesper.R:106:26:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-gesper.R#L106) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::filter(!is.na(GeneSymbol))
                         ^~~~~~~~~~
```
[R/inference-gesper.R:118:26:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-gesper.R#L118) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::select(Virus, GeneSymbol, Entrez, siRNAIDs, Readout) %>%
                         ^~~~~~~~~~
```
[R/inference-gesper.R:118:46:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-gesper.R#L118) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::select(Virus, GeneSymbol, Entrez, siRNAIDs, Readout) %>%
                                             ^~~~~~~~
```
[R/inference-gesper.R:119:13:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-gesper.R#L119) *style:* **Variable and function names should be all lowercase.**
```r
    .[order(siRNAIDs)]
            ^~~~~~~~
```
[R/inference-gesper.R:122:44:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-gesper.R#L122) *style:* **Variable and function names should be all lowercase.**
```r
  pheno.sirnas   <- as.character(pheno.mat$siRNAIDs)
                                           ^~~~~~~~
```
[R/inference-gesper.R:168:48:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-gesper.R#L168) *style:* **Variable and function names should be all lowercase.**
```r
                            siRNAIDs=pheno.mat$siRNAIDs,
                                               ^~~~~~~~
```
[R/inference-gesper.R:175:43:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-gesper.R#L175) *style:* **Variable and function names should be all lowercase.**
```r
  assertthat::assert_that(all(pheno.frame$siRNAIDs == rel.mat@siRNAs))
                                          ^~~~~~~~
```
[R/inference-gesper.R:176:43:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-gesper.R#L176) *style:* **Variable and function names should be all lowercase.**
```r
  assertthat::assert_that(all(pheno.frame$siRNAIDs ==
                                          ^~~~~~~~
```
[R/inference-gesper.R:190:50:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-gesper.R#L190) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::mutate(siRNAIDs=strsplit(as.character(siRNAIDs), ",")) %>%
                                                 ^~~~~~~~
```
[R/inference-gesper.R:191:19:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-gesper.R#L191) *style:* **Variable and function names should be all lowercase.**
```r
    tidyr::unnest(siRNAIDs)
                  ^~~~~~~~
```
[R/inference-hyperstatistic.R:75:59:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L75) *style:* **Variable and function names should be all lowercase.**
```r
  grp.indexes <- dplyr::group_indices(obj, Virus, Screen, ReadoutType,
                                                          ^~~~~~~~~~~
```
[R/inference-hyperstatistic.R:76:39:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L76) *style:* **Variable and function names should be all lowercase.**
```r
                                      ScreenType, Library, Design, Cell)
                                      ^~~~~~~~~~
```
[R/inference-hyperstatistic.R:92:50:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L92) *style:* **Variable and function names should be all lowercase.**
```r
                                         grp.dat$ScreenType[1],
                                                 ^~~~~~~~~~
```
[R/inference-hyperstatistic.R:93:50:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L93) *style:* **Variable and function names should be all lowercase.**
```r
                                         grp.dat$ReadoutType[1],
                                                 ^~~~~~~~~~~
```
[R/inference-hyperstatistic.R:98:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L98) *style:* **lines should not be more than 80 characters.**
```r
        fr <- .do.hyperstatistic(grp.dat, padjust, summ.method, do.summarization, level)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-hyperstatistic.R:115:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L115) *style:* **lines should not be more than 80 characters.**
```r
.do.hyperstatistic <- function(obj, padjust, summ.method, do.summarization, level)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-hyperstatistic.R:125:28:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L125) *style:* **Variable and function names should be all lowercase.**
```r
                           ScreenType, ReadoutType,
                           ^~~~~~~~~~
```
[R/inference-hyperstatistic.R:125:40:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L125) *style:* **Variable and function names should be all lowercase.**
```r
                           ScreenType, ReadoutType,
                                       ^~~~~~~~~~~
```
[R/inference-hyperstatistic.R:127:35:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L127) *style:* **Variable and function names should be all lowercase.**
```r
                           Plate, RowIdx, ColIdx,
                                  ^~~~~~
```
[R/inference-hyperstatistic.R:127:43:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L127) *style:* **Variable and function names should be all lowercase.**
```r
                           Plate, RowIdx, ColIdx,
                                          ^~~~~~
```
[R/inference-hyperstatistic.R:128:28:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L128) *style:* **Variable and function names should be all lowercase.**
```r
                           GeneSymbol, Entrez, siRNAIDs) %>%
                           ^~~~~~~~~~
```
[R/inference-hyperstatistic.R:128:48:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L128) *style:* **Variable and function names should be all lowercase.**
```r
                           GeneSymbol, Entrez, siRNAIDs) %>%
                                               ^~~~~~~~
```
[R/inference-hyperstatistic.R:145:21:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L145) *style:* **Variable and function names should be all lowercase.**
```r
                    ReadoutType, ScreenType,
                    ^~~~~~~~~~~
```
[R/inference-hyperstatistic.R:145:34:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L145) *style:* **Variable and function names should be all lowercase.**
```r
                    ReadoutType, ScreenType,
                                 ^~~~~~~~~~
```
[R/inference-hyperstatistic.R:147:35:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L147) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::mutate(HRes=.hypertest(GeneSymbol, siRNAIDs, Plate,
                                  ^~~~~~~~~~
```
[R/inference-hyperstatistic.R:147:47:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L147) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::mutate(HRes=.hypertest(GeneSymbol, siRNAIDs, Plate,
                                              ^~~~~~~~
```
[R/inference-hyperstatistic.R:148:35:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L148) *style:* **Variable and function names should be all lowercase.**
```r
                                  RowIdx, ColIdx, Readout, level)) %>%
                                  ^~~~~~
```
[R/inference-hyperstatistic.R:148:43:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L148) *style:* **Variable and function names should be all lowercase.**
```r
                                  RowIdx, ColIdx, Readout, level)) %>%
                                          ^~~~~~
```
[R/inference-hyperstatistic.R:157:27:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L157) *style:* **Variable and function names should be all lowercase.**
```r
  data.table::setDT(res)[,HyperRank := cumsum(res$Hit)]
                          ^~~~~~~~~
```
[R/inference-hyperstatistic.R:158:36:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L158) *style:* **Variable and function names should be all lowercase.**
```r
  data.table::setDT(res)[Hit == 0, HyperRank := NA_integer_]
                                   ^~~~~~~~~
```
[R/inference-hyperstatistic.R:179:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L179) *style:* **lines should not be more than 80 characters.**
```r
  ## if we do the hypergeometric test on genes we need another grouping as for siRNAs
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-hyperstatistic.R:187:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L187) *style:* **lines should not be more than 80 characters.**
```r
  # (the siRNA SHOULD be identical to grouping by plate/row/col; so the last grouping should be redundant)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-hyperstatistic.R:213:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-hyperstatistic.R#L213) *style:* **lines should not be more than 80 characters.**
```r
    prob <- stats::phyper(i - 1, ranks[i], N - ranks[i], ndrawn, lower.tail = F, log.p=F)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-lmm_locfdr.R:43:49:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L43) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
       gene.pathogen.matrix=gene.pathogen.matrix )
                                                ^
```
[R/inference-lmm_locfdr.R:84:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L84) *style:* **Use <-, not =, for assignment.**
```r
  call = match.call()
       ^
```
[R/inference-lmm_locfdr.R:101:13:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L101) *style:* **Use <-, not =, for assignment.**
```r
        med = median(zz)
            ^
```
[R/inference-lmm_locfdr.R:102:12:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L102) *style:* **Use <-, not =, for assignment.**
```r
        ra = med + (1 - pct) * (range(zz) - med)
           ^
```
[R/inference-lmm_locfdr.R:103:12:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L103) *style:* **Use <-, not =, for assignment.**
```r
        lo = ra[1]
           ^
```
[R/inference-lmm_locfdr.R:104:12:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L104) *style:* **Use <-, not =, for assignment.**
```r
        up = ra[2]
           ^
```
[R/inference-lmm_locfdr.R:141:9:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L141) *style:* **Use <-, not =, for assignment.**
```r
    fp0 = matrix(NA, 6, 4)
        ^
```
[R/inference-lmm_locfdr.R:142:19:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L142) *style:* **Use <-, not =, for assignment.**
```r
    colnames(fp0) = c("delta", "sigleft", "p0", "sigright")
                  ^
```
[R/inference-lmm_locfdr.R:145:9:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L145) *style:* **Use <-, not =, for assignment.**
```r
    fp0 = matrix(NA, 6, 3)
        ^
```
[R/inference-lmm_locfdr.R:146:19:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L146) *style:* **Use <-, not =, for assignment.**
```r
    colnames(fp0) = c("delta", "sigma", "p0")
                  ^
```
[R/inference-lmm_locfdr.R:148:17:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L148) *style:* **Use <-, not =, for assignment.**
```r
  rownames(fp0) = c("thest", "theSD", "mlest", "mleSD", "cmest",  "cmeSD")
                ^
```
[R/inference-lmm_locfdr.R:149:21:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L149) *style:* **Use <-, not =, for assignment.**
```r
  fp0["thest", 1:2] = c(0, 1)
                    ^
```
[R/inference-lmm_locfdr.R:150:21:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L150) *style:* **Use <-, not =, for assignment.**
```r
  fp0["theSD", 1:2] = 0
                    ^
```
[R/inference-lmm_locfdr.R:176:13:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L176) *style:* **Use <-, not =, for assignment.**
```r
    cmerror = I(is.na(co[3]) | is.na(co[2]))
            ^
```
[R/inference-lmm_locfdr.R:178:15:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L178) *style:* **Use <-, not =, for assignment.**
```r
      cmerror = I(co[2] >= 0 | co[2] + co[3] >= 0)
              ^
```
[R/inference-lmm_locfdr.R:181:13:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L181) *style:* **Use <-, not =, for assignment.**
```r
    cmerror = is.na(co[3])
            ^
```
[R/inference-lmm_locfdr.R:183:15:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L183) *style:* **Use <-, not =, for assignment.**
```r
      cmerror = I(co[3] >= 0)
              ^
```
[R/inference-lmm_locfdr.R:213:5:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L213) *style:* **Use <-, not =, for assignment.**
```r
  b = 4.3 * exp(-0.26 * log(N, 10))
    ^
```
[R/inference-lmm_locfdr.R:215:9:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L215) *style:* **Use <-, not =, for assignment.**
```r
    med = median(zz)
        ^
```
[R/inference-lmm_locfdr.R:216:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L216) *style:* **Use <-, not =, for assignment.**
```r
    sc = diff(quantile(zz)[c(2, 4)])/(2 * stats::qnorm(0.75))
       ^
```
[R/inference-lmm_locfdr.R:217:12:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L217) *style:* **Use <-, not =, for assignment.**
```r
    mlests = locmle(zz, xlim = c(med, b * sc))
           ^
```
[R/inference-lmm_locfdr.R:219:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L219) *style:* **lines should not be more than 80 characters.**
```r
      warning("length(zz) > 500,000: For ML estimation, a wider interval than optimal was used.  To use the optimal interval, rerun with mlests = c(",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-lmm_locfdr.R:221:14:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L221) *style:* **Use <-, not =, for assignment.**
```r
      mlests = locmle(zz, xlim = c(med, sc))
             ^
```
[R/inference-lmm_locfdr.R:226:9:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L226) *style:* **Use <-, not =, for assignment.**
```r
      b = 1
        ^
```
[R/inference-lmm_locfdr.R:228:14:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L228) *style:* **Use <-, not =, for assignment.**
```r
      Cov.in = list(x = x, X = X, f = f, sw = sw)
             ^
```
[R/inference-lmm_locfdr.R:229:14:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L229) *style:* **Use <-, not =, for assignment.**
```r
      ml.out = locmle(zz, xlim = c(mlests[1], b * mlests[2]),
             ^
```
[R/inference-lmm_locfdr.R:231:14:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L231) *style:* **Use <-, not =, for assignment.**
```r
      mlests = ml.out$mle
             ^
```
[R/inference-lmm_locfdr.R:233:17:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L233) *style:* **Use <-, not =, for assignment.**
```r
    else mlests = locmle(zz, xlim = c(mlests[1], b * mlests[2]),
                ^
```
[R/inference-lmm_locfdr.R:235:23:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L235) *style:* **Use <-, not =, for assignment.**
```r
    fp0["mlest", 1:3] = mlests[1:3]
                      ^
```
[R/inference-lmm_locfdr.R:236:23:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L236) *style:* **Use <-, not =, for assignment.**
```r
    fp0["mleSD", 1:3] = mlests[4:6]
                      ^
```
[R/inference-lmm_locfdr.R:240:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L240) *style:* **lines should not be more than 80 characters.**
```r
                                                              2]/mlests[2])) > 0.05)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-lmm_locfdr.R:241:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L241) *style:* **lines should not be more than 80 characters.**
```r
      warning("Discrepancy between central matching and maximum likelihood estimates.\nConsider rerunning with nulltype = 1")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-lmm_locfdr.R:251:12:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L251) *style:* **Use <-, not =, for assignment.**
```r
    delhat = xmax = xmaxx = mlests[1]
           ^
```
[R/inference-lmm_locfdr.R:251:19:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L251) *style:* **Use <-, not =, for assignment.**
```r
    delhat = xmax = xmaxx = mlests[1]
                  ^
```
[R/inference-lmm_locfdr.R:251:27:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L251) *style:* **Use <-, not =, for assignment.**
```r
    delhat = xmax = xmaxx = mlests[1]
                          ^
```
[R/inference-lmm_locfdr.R:252:12:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L252) *style:* **Use <-, not =, for assignment.**
```r
    sighat = mlests[2]
           ^
```
[R/inference-lmm_locfdr.R:253:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L253) *style:* **Use <-, not =, for assignment.**
```r
    p0 = mlests[3]
       ^
```
[R/inference-lmm_locfdr.R:254:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L254) *style:* **Use <-, not =, for assignment.**
```r
    f0 = stats::dnorm(x, delhat, sighat)
       ^
```
[R/inference-lmm_locfdr.R:255:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L255) *style:* **Use <-, not =, for assignment.**
```r
    f0 = (sum(f) * f0)/sum(f0)
       ^
```
[R/inference-lmm_locfdr.R:257:7:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L257) *style:* **Use <-, not =, for assignment.**
```r
  fdr = pmin((p0 * f0)/f, 1)
      ^
```
[R/inference-lmm_locfdr.R:261:19:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L261) *style:* **Use <-, not =, for assignment.**
```r
  fp0["thest", 3] = p0theo
                  ^
```
[R/inference-lmm_locfdr.R:273:13:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L273) *style:* **Use <-, not =, for assignment.**
```r
  else xxlo = xmax
            ^
```
[R/inference-lmm_locfdr.R:276:13:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L276) *style:* **Use <-, not =, for assignment.**
```r
  else xxhi = xmax
            ^
```
[R/inference-lmm_locfdr.R:281:13:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L281) *style:* **Use <-, not =, for assignment.**
```r
  else xxlo = xmax
            ^
```
[R/inference-lmm_locfdr.R:284:13:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L284) *style:* **Use <-, not =, for assignment.**
```r
  else xxhi = xmax
            ^
```
[R/inference-lmm_locfdr.R:288:66:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L288) *style:* **Use <-, not =, for assignment.**
```r
    fdr[x >= mlests[1] - mlests[2] & x <= mlests[1] + mlests[2]] = 1
                                                                 ^
```
[R/inference-lmm_locfdr.R:289:67:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L289) *style:* **Use <-, not =, for assignment.**
```r
    fdr0[x >= mlests[1] - mlests[2] & x <= mlests[1] + mlests[2]] = 1
                                                                  ^
```
[R/inference-lmm_locfdr.R:300:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L300) *style:* **lines should not be more than 80 characters.**
```r
                                                             fdr[ido]) * fall[ido])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-lmm_locfdr.R:302:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L302) *style:* **lines should not be more than 80 characters.**
```r
                                                                fdr0[ido]) * fall[ido])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-lmm_locfdr.R:304:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L304) *style:* **lines should not be more than 80 characters.**
```r
                                                              fdr[iup]) * fall[iup])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-lmm_locfdr.R:306:1:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L306) *style:* **lines should not be more than 80 characters.**
```r
                                                                 fdr0[iup]) * fall[iup])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference-lmm_locfdr.R:308:28:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L308) *style:* **Use <-, not =, for assignment.**
```r
  Efdr[which(is.na(Efdr))] = 1
                           ^
```
[R/inference-lmm_locfdr.R:315:9:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L315) *style:* **Use <-, not =, for assignment.**
```r
    mul = c(1, mult)
        ^
```
[R/inference-lmm_locfdr.R:316:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L316) *style:* **Use <-, not =, for assignment.**
```r
    EE = rep(0, length(mul))
       ^
```
[R/inference-lmm_locfdr.R:318:10:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L318) *style:* **Use <-, not =, for assignment.**
```r
      xe = sqrt(mul[m]) * x
         ^
```
[R/inference-lmm_locfdr.R:319:11:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L319) *style:* **Use <-, not =, for assignment.**
```r
      f1e = approx(xe, f1, x, rule = 2, ties = mean)$y
          ^
```
[R/inference-lmm_locfdr.R:320:11:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L320) *style:* **Use <-, not =, for assignment.**
```r
      f1e = (f1e * sum(f1))/sum(f1e)
          ^
```
[R/inference-lmm_locfdr.R:321:11:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L321) *style:* **Use <-, not =, for assignment.**
```r
      f0e = f0
          ^
```
[R/inference-lmm_locfdr.R:322:11:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L322) *style:* **Use <-, not =, for assignment.**
```r
      p0e = p0
          ^
```
[R/inference-lmm_locfdr.R:324:13:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L324) *style:* **Use <-, not =, for assignment.**
```r
        f0e = f00
            ^
```
[R/inference-lmm_locfdr.R:325:13:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L325) *style:* **Use <-, not =, for assignment.**
```r
        p0e = p0theo
            ^
```
[R/inference-lmm_locfdr.R:327:12:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L327) *style:* **Use <-, not =, for assignment.**
```r
      fdre = (p0e * f0e)/(p0e * f0e + f1e)
           ^
```
[R/inference-lmm_locfdr.R:328:13:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L328) *style:* **Use <-, not =, for assignment.**
```r
      EE[m] = sum(f1e * fdre)/sum(f1e)
            ^
```
[R/inference-lmm_locfdr.R:330:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L330) *style:* **Use <-, not =, for assignment.**
```r
    EE = EE/EE[1]
       ^
```
[R/inference-lmm_locfdr.R:331:15:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L331) *style:* **Use <-, not =, for assignment.**
```r
    names(EE) = mul
              ^
```
[R/inference-lmm_locfdr.R:333:12:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L333) *style:* **Use <-, not =, for assignment.**
```r
  Cov2.out = loccov2(X, X0, i0, f, fp0["cmest", ], N)
           ^
```
[R/inference-lmm_locfdr.R:334:12:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L334) *style:* **Use <-, not =, for assignment.**
```r
  Cov0.out = loccov2(X, matrix(1, length(x), 1), i0, f, fp0["thest",
           ^
```
[R/inference-lmm_locfdr.R:338:13:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L338) *style:* **Use <-, not =, for assignment.**
```r
      Ilfdr = Cov0.out$Ilfdr
            ^
```
[R/inference-lmm_locfdr.R:340:13:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L340) *style:* **Use <-, not =, for assignment.**
```r
      Ilfdr = ml.out$Ilfdr
            ^
```
[R/inference-lmm_locfdr.R:342:13:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L342) *style:* **Use <-, not =, for assignment.**
```r
      Ilfdr = Cov2.out$Ilfdr
            ^
```
[R/inference-lmm_locfdr.R:347:9:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L347) *style:* **Use <-, not =, for assignment.**
```r
    Cov = Cov0.out$Cov
        ^
```
[R/inference-lmm_locfdr.R:349:9:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L349) *style:* **Use <-, not =, for assignment.**
```r
    Cov = ml.out$Cov.lfdr
        ^
```
[R/inference-lmm_locfdr.R:350:12:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L350) *style:* **Use <-, not =, for assignment.**
```r
  else Cov = Cov2.out$Cov
           ^
```
[R/inference-lmm_locfdr.R:352:21:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L352) *style:* **Use <-, not =, for assignment.**
```r
  fp0["cmeSD", 1:3] = Cov2.out$stdev[c(2, 3, 1)]
                    ^
```
[R/inference-lmm_locfdr.R:354:21:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L354) *style:* **Use <-, not =, for assignment.**
```r
    fp0["cmeSD", 4] = fp0["cmeSD", 2]
                    ^
```
[R/inference-lmm_locfdr.R:355:19:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L355) *style:* **Use <-, not =, for assignment.**
```r
  fp0["theSD", 3] = Cov0.out$stdev[1]
                  ^
```
[R/inference-lmm_locfdr.R:358:11:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L358) *style:* **Use <-, not =, for assignment.**
```r
      pds = fp0["thest", c(3, 1, 2)]
          ^
```
[R/inference-lmm_locfdr.R:359:13:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L359) *style:* **Use <-, not =, for assignment.**
```r
      stdev = fp0["theSD", c(3, 1, 2)]
            ^
```
[R/inference-lmm_locfdr.R:360:12:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L360) *style:* **Use <-, not =, for assignment.**
```r
      pds. = t(Cov0.out$pds.)
           ^
```
[R/inference-lmm_locfdr.R:363:11:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L363) *style:* **Use <-, not =, for assignment.**
```r
      pds = fp0["mlest", c(3, 1, 2)]
          ^
```
[R/inference-lmm_locfdr.R:364:13:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L364) *style:* **Use <-, not =, for assignment.**
```r
      stdev = fp0["mleSD", c(3, 1, 2)]
            ^
```
[R/inference-lmm_locfdr.R:365:12:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L365) *style:* **Use <-, not =, for assignment.**
```r
      pds. = t(ml.out$pds.)
           ^
```
[R/inference-lmm_locfdr.R:368:11:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L368) *style:* **Use <-, not =, for assignment.**
```r
      pds = fp0["cmest", c(3, 1, 2)]
          ^
```
[R/inference-lmm_locfdr.R:369:13:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L369) *style:* **Use <-, not =, for assignment.**
```r
      stdev = fp0["cmeSD", c(3, 1, 2)]
            ^
```
[R/inference-lmm_locfdr.R:370:12:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L370) *style:* **Use <-, not =, for assignment.**
```r
      pds. = t(Cov2.out$pds.)
           ^
```
[R/inference-lmm_locfdr.R:373:20:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L373) *style:* **Use <-, not =, for assignment.**
```r
    colnames(pds.) = names(pds) = c("p0", "delhat", "sighat")
                   ^
```
[R/inference-lmm_locfdr.R:373:33:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L373) *style:* **Use <-, not =, for assignment.**
```r
    colnames(pds.) = names(pds) = c("p0", "delhat", "sighat")
                                ^
```
[R/inference-lmm_locfdr.R:374:18:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L374) *style:* **Use <-, not =, for assignment.**
```r
    names(stdev) = c("sdp0", "sddelhat", "sdsighat")
                 ^
```
[R/inference-lmm_locfdr.R:391:7:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L391) *style:* **Use <-, not =, for assignment.**
```r
  z.2 = rep(NA, 2)
      ^
```
[R/inference-lmm_locfdr.R:392:5:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L392) *style:* **Use <-, not =, for assignment.**
```r
  m = order(fd)[nx]
    ^
```
[R/inference-lmm_locfdr.R:394:12:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L394) *style:* **Use <-, not =, for assignment.**
```r
    z.2[2] = stats::approx(fd[m:nx], x[m:nx], 0.2, ties = mean)$y
           ^
```
[R/inference-lmm_locfdr.R:397:12:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L397) *style:* **Use <-, not =, for assignment.**
```r
    z.2[1] = stats::approx(fd[1:m], x[1:m], 0.2, ties = mean)$y
           ^
```
[R/inference-lmm_locfdr.R:411:6:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L411) *style:* **Use <-, not =, for assignment.**
```r
  vl = list(fdr = ffdr, fp0 = fp0, Efdr = Efdr, cdf1 = cdf1,
     ^
```
[R/inference-lmm_locfdr.R:414:13:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L414) *style:* **Use <-, not =, for assignment.**
```r
    vl$mult = EE
            ^
```
[R/inference-lmm_locfdr.R:415:11:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L415) *style:* **Use <-, not =, for assignment.**
```r
  vl$call = call
          ^
```
[R/inference-lmm_locfdr.R:426:5:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L426) *style:* **Use <-, not =, for assignment.**
```r
  N = length(z)
    ^
```
[R/inference-lmm_locfdr.R:429:9:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L429) *style:* **Use <-, not =, for assignment.**
```r
      b = 1
        ^
```
[R/inference-lmm_locfdr.R:430:12:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L430) *style:* **Use <-, not =, for assignment.**
```r
    else b = 4.3 * exp(-0.26 * log(N, 10))
           ^
```
[R/inference-lmm_locfdr.R:431:10:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L431) *style:* **Use <-, not =, for assignment.**
```r
    xlim = c(median(z), b * diff(quantile(z)[c(2, 4)])/(2 *
         ^
```
[R/inference-lmm_locfdr.R:434:9:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L434) *style:* **Use <-, not =, for assignment.**
```r
  aorig = xlim[1] - xlim[2]
        ^
```
[R/inference-lmm_locfdr.R:435:9:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L435) *style:* **Use <-, not =, for assignment.**
```r
  borig = xlim[1] + xlim[2]
        ^
```
[R/inference-lmm_locfdr.R:436:6:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L436) *style:* **Use <-, not =, for assignment.**
```r
  z0 = z[which(z >= aorig & z <= borig)]
     ^
```
[R/inference-lmm_locfdr.R:437:6:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L437) *style:* **Use <-, not =, for assignment.**
```r
  N0 = length(z0)
     ^
```
[R/inference-lmm_locfdr.R:438:5:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L438) *style:* **Use <-, not =, for assignment.**
```r
  Y = c(mean(z0), mean(z0^2))
    ^
```
[R/inference-lmm_locfdr.R:439:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L439) *style:* **Use <-, not =, for assignment.**
```r
  that = N0/N
       ^
```
[R/inference-lmm_locfdr.R:441:9:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L441) *style:* **Use <-, not =, for assignment.**
```r
    bet = c(d/s^2, -1/(2 * s^2))
        ^
```
[R/inference-lmm_locfdr.R:442:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L442) *style:* **Use <-, not =, for assignment.**
```r
    aa = (aorig - d)/s
       ^
```
[R/inference-lmm_locfdr.R:443:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L443) *style:* **Use <-, not =, for assignment.**
```r
    bb = (borig - d)/s
       ^
```
[R/inference-lmm_locfdr.R:444:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L444) *style:* **Use <-, not =, for assignment.**
```r
    H0 = pnorm(bb) - pnorm(aa)
       ^
```
[R/inference-lmm_locfdr.R:445:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L445) *style:* **Use <-, not =, for assignment.**
```r
    fa = dnorm(aa)
       ^
```
[R/inference-lmm_locfdr.R:446:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L446) *style:* **Use <-, not =, for assignment.**
```r
    fb = dnorm(bb)
       ^
```
[R/inference-lmm_locfdr.R:447:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L447) *style:* **Use <-, not =, for assignment.**
```r
    H1 = fa - fb
       ^
```
[R/inference-lmm_locfdr.R:448:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L448) *style:* **Use <-, not =, for assignment.**
```r
    H2 = H0 + aa * fa - bb * fb
       ^
```
[R/inference-lmm_locfdr.R:449:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L449) *style:* **Use <-, not =, for assignment.**
```r
    H3 = (2 + aa^2) * fa - (2 + bb^2) * fb
       ^
```
[R/inference-lmm_locfdr.R:450:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L450) *style:* **Use <-, not =, for assignment.**
```r
    H4 = 3 * H0 + (3 * aa + aa^3) * fa - (3 * bb + bb^3) *
       ^
```
[R/inference-lmm_locfdr.R:452:7:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L452) *style:* **Use <-, not =, for assignment.**
```r
    H = c(H0, H1, H2, H3, H4)
      ^
```
[R/inference-lmm_locfdr.R:453:7:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L453) *style:* **Use <-, not =, for assignment.**
```r
    r = d/s
      ^
```
[R/inference-lmm_locfdr.R:454:7:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L454) *style:* **Use <-, not =, for assignment.**
```r
    I = matrix(rep(0, 25), 5)
      ^
```
[R/inference-lmm_locfdr.R:455:40:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L455) *style:* **Use <-, not =, for assignment.**
```r
    for (i in 0:4) I[i + 1, 0:(i + 1)] = choose(i, 0:i)
                                       ^
```
[R/inference-lmm_locfdr.R:456:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L456) *style:* **Use <-, not =, for assignment.**
```r
    u1 = s^(0:4)
       ^
```
[R/inference-lmm_locfdr.R:457:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L457) *style:* **Use <-, not =, for assignment.**
```r
    II = pmax(row(I) - col(I), 0)
       ^
```
[R/inference-lmm_locfdr.R:458:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L458) *style:* **Use <-, not =, for assignment.**
```r
    II = r^II
       ^
```
[R/inference-lmm_locfdr.R:459:7:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L459) *style:* **Use <-, not =, for assignment.**
```r
    I = u1 * (I * II)
      ^
```
[R/inference-lmm_locfdr.R:460:7:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L460) *style:* **Use <-, not =, for assignment.**
```r
    E = as.vector(I %*% H)/H0
      ^
```
[R/inference-lmm_locfdr.R:461:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L461) *style:* **Use <-, not =, for assignment.**
```r
    E1 = E[2]
       ^
```
[R/inference-lmm_locfdr.R:462:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L462) *style:* **Use <-, not =, for assignment.**
```r
    E2 = E[3]
       ^
```
[R/inference-lmm_locfdr.R:463:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L463) *style:* **Use <-, not =, for assignment.**
```r
    E3 = E[4]
       ^
```
[R/inference-lmm_locfdr.R:464:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L464) *style:* **Use <-, not =, for assignment.**
```r
    E4 = E[5]
       ^
```
[R/inference-lmm_locfdr.R:465:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L465) *style:* **Use <-, not =, for assignment.**
```r
    mu = c(E1, E2)
       ^
```
[R/inference-lmm_locfdr.R:466:7:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L466) *style:* **Use <-, not =, for assignment.**
```r
    V = matrix(c(E2 - E1^2, E3 - E1 * E2, E3 - E1 * E2, E4 -
      ^
```
[R/inference-lmm_locfdr.R:468:10:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L468) *style:* **Use <-, not =, for assignment.**
```r
    bett = bet + solve(V, Y - mu)/(1 + 1/j^2)
         ^
```
[R/inference-lmm_locfdr.R:470:12:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L470) *style:* **Use <-, not =, for assignment.**
```r
      bett = bet + 0.1 * solve(V, Y - mu)/(1 + 1/j^2)
           ^
```
[R/inference-lmm_locfdr.R:475:7:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L475) *style:* **Use <-, not =, for assignment.**
```r
    d = -bett[1]/(2 * bett[2])
      ^
```
[R/inference-lmm_locfdr.R:476:7:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L476) *style:* **Use <-, not =, for assignment.**
```r
    s = 1/sqrt(-2 * bett[2])
      ^
```
[R/inference-lmm_locfdr.R:481:9:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L481) *style:* **Use <-, not =, for assignment.**
```r
    mle = rep(NA, 6)
        ^
```
[R/inference-lmm_locfdr.R:482:14:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L482) *style:* **Use <-, not =, for assignment.**
```r
    Cov.lfdr = NA
             ^
```
[R/inference-lmm_locfdr.R:483:9:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L483) *style:* **Use <-, not =, for assignment.**
```r
    Cor = matrix(NA, 3, 3)
        ^
```
[R/inference-lmm_locfdr.R:486:9:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L486) *style:* **Use <-, not =, for assignment.**
```r
    mle = rep(NA, 6)
        ^
```
[R/inference-lmm_locfdr.R:487:14:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L487) *style:* **Use <-, not =, for assignment.**
```r
    Cov.lfdr = Cov.out = NA
             ^
```
[R/inference-lmm_locfdr.R:487:24:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L487) *style:* **Use <-, not =, for assignment.**
```r
    Cov.lfdr = Cov.out = NA
                       ^
```
[R/inference-lmm_locfdr.R:488:9:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L488) *style:* **Use <-, not =, for assignment.**
```r
    Cor = matrix(NA, 3, 3)
        ^
```
[R/inference-lmm_locfdr.R:491:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L491) *style:* **Use <-, not =, for assignment.**
```r
    aa = (aorig - d)/s
       ^
```
[R/inference-lmm_locfdr.R:492:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L492) *style:* **Use <-, not =, for assignment.**
```r
    bb = (borig - d)/s
       ^
```
[R/inference-lmm_locfdr.R:493:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L493) *style:* **Use <-, not =, for assignment.**
```r
    H0 = pnorm(bb) - pnorm(aa)
       ^
```
[R/inference-lmm_locfdr.R:494:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L494) *style:* **Use <-, not =, for assignment.**
```r
    p0 = that/H0
       ^
```
[R/inference-lmm_locfdr.R:495:7:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L495) *style:* **Use <-, not =, for assignment.**
```r
    J = s^2 * matrix(c(1, 0, 2 * d, s), 2)
      ^
```
[R/inference-lmm_locfdr.R:496:8:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L496) *style:* **Use <-, not =, for assignment.**
```r
    JV = J %*% solve(V)
       ^
```
[R/inference-lmm_locfdr.R:497:9:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L497) *style:* **Use <-, not =, for assignment.**
```r
    JVJ = JV %*% t(J)
        ^
```
[R/inference-lmm_locfdr.R:498:10:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L498) *style:* **Use <-, not =, for assignment.**
```r
    mat2 = cbind(0, JVJ/N0)
         ^
```
[R/inference-lmm_locfdr.R:499:10:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L499) *style:* **Use <-, not =, for assignment.**
```r
    mat1 = c((p0 * H0 * (1 - p0 * H0))/N, 0, 0)
         ^
```
[R/inference-lmm_locfdr.R:500:9:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L500) *style:* **Use <-, not =, for assignment.**
```r
    mat = rbind(mat1, mat2)
        ^
```
[R/inference-lmm_locfdr.R:501:7:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L501) *style:* **Use <-, not =, for assignment.**
```r
    h = c(H1/H0, (H2 - H0)/H0)
      ^
```
[R/inference-lmm_locfdr.R:502:10:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L502) *style:* **Use <-, not =, for assignment.**
```r
    matt = c(1/H0, -(p0/s) * t(h))
         ^
```
[R/inference-lmm_locfdr.R:503:10:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L503) *style:* **Use <-, not =, for assignment.**
```r
    matt = rbind(matt, cbind(0, diag(2)))
         ^
```
[R/inference-lmm_locfdr.R:504:7:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L504) *style:* **Use <-, not =, for assignment.**
```r
    C = matt %*% (mat %*% t(matt))
      ^
```
[R/inference-lmm_locfdr.R:505:9:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L505) *style:* **Use <-, not =, for assignment.**
```r
    mle = c(p0, d, s, diag(C)^0.5)
        ^
```
[R/inference-lmm_locfdr.R:507:10:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L507) *style:* **Use <-, not =, for assignment.**
```r
      sd = mle[4:6]
         ^
```
[R/inference-lmm_locfdr.R:508:10:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L508) *style:* **Use <-, not =, for assignment.**
```r
      Co = C/outer(sd, sd)
         ^
```
[R/inference-lmm_locfdr.R:509:20:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L509) *style:* **Use <-, not =, for assignment.**
```r
      dimnames(Co) = list(c("p0", "d", "s"), c("p0", "d",
                   ^
```
[R/inference-lmm_locfdr.R:511:11:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L511) *style:* **Use <-, not =, for assignment.**
```r
      Cor = Co[c(2, 3, 1), c(2, 3, 1)]
          ^
```
[R/inference-lmm_locfdr.R:514:10:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L514) *style:* **Use <-, not =, for assignment.**
```r
      i0 = which(Cov.in$x > aa & Cov.in$x < bb)
         ^
```
[R/inference-lmm_locfdr.R:515:15:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L515) *style:* **Use <-, not =, for assignment.**
```r
      Cov.out = loccov(N, N0, p0, d, s, Cov.in$x, Cov.in$X,
              ^
```
[R/inference-lmm_locfdr.R:519:14:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L519) *style:* **Use <-, not =, for assignment.**
```r
  names(mle) = c("p0", "del0", "sig0", "sd.p0", "sd.del0",
             ^
```
[R/inference-lmm_locfdr.R:521:7:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L521) *style:* **Use <-, not =, for assignment.**
```r
  mle = mle[c(2, 3, 1, 5, 6, 4)]
      ^
```
[R/inference-lmm_locfdr.R:522:7:](https://github.com/dirmeier/knockout/blob/ba9d8cf69d12ce748a7396757e429258869e1607/R/inference-lmm_locfdr.R#L522) *style:* **Use <-, not =, for assignment.**
```r
  out = list(mle = mle)
      ^
```


TeamCity Platform Services :: Environment Manager 2 :: Package [Build 3.37.2-pre-21-g0e4dcbb](http://infra.teamcity.ci.ttldev/viewLog.html?buildId=55092&buildTypeId=PlatformServices_EnvironmentManager2_Package) outcome was **SUCCESS**
Summary: Running Build time: 00:00:57


Hier müsste einmal definiert werden was übergeben werden soll.
Aktuell kann hier "Deutschland", "Germany" und "DE" übergeben werden. Bei anderen Ländern geht die deutsche Variante aber nicht (Je nachdem was in der DB (Tabelle "stamd_land") steht.


Хорошо, только не совсем понял логики действия. Правильно ли понимаю, что надо у пользователя спросить какой вагон присоединять? И если выбрал неправильный тип, не присоединять и наоборот?


I will, when I start tagging them 😉 The duplicate RemoteFiles is probably a merge artefact. Good catch!


Mike, you're speaking Greek. I barely got through the DOM section alive.


wtf


Joli travail, j'aime beaucoup <3


`class a{
 String name;
}`


Makes sense, thanks.


I would change this condition to also point to `how_much_expect_to_claim?` and then change it when `car_status_before_usage?` is implemented in the next commit. That way all of the tests will continue to pass.


adv-ss-nv-docs (jasondegraw) - x86_64-Linux-Ubuntu-14.04-gcc-4.8: Tests Failed (616 of 2520 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-24.44%25-red.png)


aa


TeamCity Platform Services :: Environment Manager 2 :: Package [Build 3.37.2-pre-12-gb2520b3](http://infra.teamcity.ci.ttldev/viewLog.html?buildId=55096&buildTypeId=PlatformServices_EnvironmentManager2_Package) outcome was **SUCCESS**
Summary: Running Build time: 00:00:48


Hier sollten wir vielleicht noch das Attribut "apikey" hinzufügen (Sowie ins PHP-SDK), damit die Kunden auch von der alten Schnittstelle zur neuen wechseln können.


adv-ss-nv-docs (jasondegraw) - x86_64-Linux-Ubuntu-14.04-custom_check: OK (0 of 0 tests passed, 0 test warnings)

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


ExtraQuestionSeed = int64(0) << is this always 0?


Не совсем согласен с названиями.
Мой redis_client_wrapp  - это же обертка вокруг конкретной реализации redisclient.
Вот этот код совершенно не обобщенный, в другой реализации будет другой интерфейс.
client.command("GET", {key}, [this, &data, &get_handler](const auto &client_value) {
                data = to_string(client_value);
                get_handler(this->io, data);
            });
Поэтому я и не делал его шаблонным и назвал именно redis_client. Wrapper (возможно надо было назвать adapter) задумывался как обертка вокруг конкретных asio клиентов, wrapper реализует интерфейс которым пользуется key_value_client, поэтому я их и разделил.

Согласен, что для key_value_client более удачное название asio_key_value_client.

Я думал, что kv_connection_pool, asio_key_value_client - могут пойти в core/vanilla-rtb
Плюс добавить туда :
class asio_dummy_client_wrapp {
    public:
        using connection_ok_handler_type = std::function<void(boost::asio::io_service&)>;
        using connection_fail_handler_type = std::function<void(const std::string&, boost::asio::io_service&)>;
        using get_handler_type = std::function<void(boost::asio::io_service&, const std::string&)>;

        redis_client_wrapp(boost::asio::io_service &io):
            io{io}, client{io}
        {}
        void connect(const std::string &host, uint16_t port, const connection_ok_handler_type &connection_ok_handler, const connection_fail_handler_type &connection_fail_handler) {
            connection_fail_handler(err, this->io);
        }
       // Should never be called, because always disconnected
        void get(const std::string &key, std::string &data, const get_handler_type &get_handler) {
                get_handler(this->io, data);
        }
        bool connected() const {
            return false;
        }
    private:
        boost::asio::io_service &io;
        redisclient::RedisAsyncClient client;
    };

Или то, что я требую чтобы клиенты были на основе asio - слишком сильное требование?


Besoin d'une version non releasée de core. C'est normal.


Das müsste auch wieder weg.


There is no error code. Just device manager is as follows.
There is no RTrobot servo driver files in C:\Program Files (x86) or C:\Program Files  after installing ServoController_Windows_3.1.5\Windows\Servos Controller Drive.exe.
When this file ervos Controller Drive.exe. is installed, what kind files are installed? Instead of Servos Controller Drive.exe., can you share the driver files(dll, ini, etc)?
I'll try to install the driver directly through device manager.


Understood.  Is there a policy as to who will update the Changes?  I've worked under the general assumption that the release manager does that.  In this case, do you prefer that the contributer does?


I was unsure if we should move them out as well (a bit of the same reasons that you have mention) but since we have the same config copied around I did find it more convenient to move them. The reason to spit them into oracle and h2 was just to make it more clear where they're used.
Since you didn't replied on my comment on slack I kinda figured you didn't disagree with my conclusion.


**Whoops!**

There were **1 critical errors** that broke the build and prevented it from being automatically deployed.

There were *2 warnings* that will prevent this PR from being merged. Please take a look, and either fix, or provide a justification for why they can't be fixed.

**ERRORS**
[`src/content/en/updates/2017/03/chrome-58-media-updates.md#L8`](https://github.com/Google/WebFundamentals/blame/ce19631d0fb49a0472fe3f2f6d6e1e71780823b5/src/content/en/updates/2017/03/chrome-58-media-updates.md#L8) - WF Tag `wf_featured_image` found, but couldn't find image - /web/updates/images/2017/03/media-updates.png

**WARNINGS**
[`src/content/en/updates/2017/03/chrome-58-media-updates.md#L53`](https://github.com/Google/WebFundamentals/blame/ce19631d0fb49a0472fe3f2f6d6e1e71780823b5/src/content/en/updates/2017/03/chrome-58-media-updates.md#L53) - Line must be at most 100 characters
[`src/content/en/updates/2017/03/chrome-58-media-updates.md#L151`](https://github.com/Google/WebFundamentals/blame/ce19631d0fb49a0472fe3f2f6d6e1e71780823b5/src/content/en/updates/2017/03/chrome-58-media-updates.md#L151) - Line must be at most 100 characters


The creation of this question should also be moved to the next commit.


the /bin/docker doesnt exists anymore as /bin/docker was removed in the commit https://github.com/avthart/docker-consul-template/commit/d11b593ad3c971d7df396d15e91f04d645fb4ae6

Now you have to run:
`-consul=127.0.0.1:8500 -wait=5s -template="/tmp/nginx.ctmpl:/etc/nginx/sites-available/default:docker kill -s HUP nginx"`


The suppression of spaces in mount point creates a bug in my server.
Here is the result of the command: `/bin/df -T -P`
`/dev/mmcblk0p1 vfat           65390     2790     62600       5% /boot`
As you can see there is a space between the first and the second column.
Here is the result of the command: `/bin/df -T -P | sed -e 's/[ \t]//'`
`/dev/mmcblk0p1vfat           65390     2790     62600       5% /boot`
As the space has been removed the columns 1 and 2 have merged, which creates the problem.
What's the point to remove spaces in mount point names?


Looks like this broke CUDA builds


Die Tests müssen wir noch rausnehmen (wegen fehlender Testbarkeit der PIN-Abfrage für die Device-Anmeldung)


I don't think the spec file is ready for full systemd support, the etc/cerebrod.systemd config does not end up the %{_unitdir} in RPM_BUILD_ROOT.  Will debug a bit more.