[R/inference_chisqstatistic.R:71:59:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_chisqstatistic.R#L71) *style:* **Variable and function names should be all lowercase.**
```r
  grp.indexes <- dplyr::group_indices(obj, Virus, Screen, ReadoutType,
                                                          ^~~~~~~~~~~
```
[R/inference_chisqstatistic.R:72:39:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_chisqstatistic.R#L72) *style:* **Variable and function names should be all lowercase.**
```r
                                      ScreenType, Library, Design, Cell)
                                      ^~~~~~~~~~
```
[R/inference_chisqstatistic.R:85:52:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_chisqstatistic.R#L85) *style:* **Variable and function names should be all lowercase.**
```r
                                           grp.dat$ScreenType[1],
                                                   ^~~~~~~~~~
```
[R/inference_chisqstatistic.R:86:52:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_chisqstatistic.R#L86) *style:* **Variable and function names should be all lowercase.**
```r
                                           grp.dat$ReadoutType[1],
                                                   ^~~~~~~~~~~
```
[R/inference_diffuse_knn.R:38:59:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse_knn.R#L38) *style:* **Variable and function names should be all lowercase.**
```r
       dplyr::filter(Idx %in% as.integer(names(neighs))))$GeneSymbol
                                                          ^~~~~~~~~~
```
[R/inference_diffuse_knn.R:43:21:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse_knn.R#L43) *style:* **Variable and function names should be all lowercase.**
```r
      dplyr::select(GeneSymbol, Effect)}
                    ^~~~~~~~~~
```
[R/inference_diffuse_knn.R:52:49:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse_knn.R#L52) *style:* **Variable and function names should be all lowercase.**
```r
  genes.found <- dplyr::select(flat.dat, Start, GeneSymbol) %>%
                                                ^~~~~~~~~~
```
[R/inference_diffuse_mrw.R:36:44:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse_mrw.R#L36) *style:* **Variable and function names should be all lowercase.**
```r
  li  <- list(diffusion=dplyr::select(res, GeneSymbol, Effect, DiffusionEffect),
                                           ^~~~~~~~~~
```
[R/inference_diffuse_mrw.R:36:64:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse_mrw.R#L36) *style:* **Variable and function names should be all lowercase.**
```r
  li  <- list(diffusion=dplyr::select(res, GeneSymbol, Effect, DiffusionEffect),
                                                               ^~~~~~~~~~~~~~~
```
[R/inference_diffuse_mrw.R:50:22:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse_mrw.R#L50) *style:* **Variable and function names should be all lowercase.**
```r
  diffuse.data$frame$DiffusionEffect <- mrw
                     ^~~~~~~~~~~~~~~
```
[R/inference_diffuse_mrw.R:72:58:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse_mrw.R#L72) *style:* **Variable and function names should be all lowercase.**
```r
  boot.g <- tidyr::gather(bootstrap.hits, Boot, Effect, -GeneSymbol) %>%
                                                         ^~~~~~~~~~
```
[R/inference_diffuse_mrw.R:85:1:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse_mrw.R#L85) *style:* **lines should not be more than 80 characters.**
```r
  # -> calculate means -> calculate alphas -> calculate variance -> calculate alpha_0
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference_diffuse_mrw.R:91:21:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse_mrw.R#L91) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::group_by(GeneSymbol) %>%
                    ^~~~~~~~~~
```
[R/inference_diffuse_mrw.R:93:29:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse_mrw.R#L93) *style:* **Variable and function names should be all lowercase.**
```r
                       mean(DiffusionEffect, na.rm=T)) %>%
                            ^~~~~~~~~~~~~~~
```
[R/inference_diffuse_mrw.R:96:57:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse_mrw.R#L96) *style:* **Variable and function names should be all lowercase.**
```r
                          tidyr::spread(flat.dat, boot, DiffusionEffect),
                                                        ^~~~~~~~~~~~~~~
```
[R/inference_diffuse.R:88:39:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse.R#L88) *style:* **Variable and function names should be all lowercase.**
```r
    hits   <- dplyr::select(obj@.data$gene.hitsGeneSymbol, abs(Effect))
                                      ^~~~~~~~~~~~~~~~~~~
```
[R/inference_diffuse.R:94:23:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse.R#L94) *style:* **Variable and function names should be all lowercase.**
```r
        dplyr::filter(GeneSymbol %in% hits$GeneSymbol) %>%
                      ^~~~~~~~~~
```
[R/inference_diffuse.R:94:44:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse.R#L94) *style:* **Variable and function names should be all lowercase.**
```r
        dplyr::filter(GeneSymbol %in% hits$GeneSymbol) %>%
                                           ^~~~~~~~~~
```
[R/inference_diffuse.R:95:24:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse.R#L95) *style:* **Variable and function names should be all lowercase.**
```r
        dplyr::select(-MeanBootstrap, -Pval, -FDR)
                       ^~~~~~~~~~~~~
```
[R/inference_diffuse.R:151:44:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse.R#L151) *style:* **Variable and function names should be all lowercase.**
```r
  li  <- list(diffusion=dplyr::select(res, GeneSymbol, Effect, DiffusionEffect),
                                           ^~~~~~~~~~
```
[R/inference_diffuse.R:151:64:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse.R#L151) *style:* **Variable and function names should be all lowercase.**
```r
  li  <- list(diffusion=dplyr::select(res, GeneSymbol, Effect, DiffusionEffect),
                                                               ^~~~~~~~~~~~~~~
```
[R/inference_diffuse.R:165:22:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse.R#L165) *style:* **Variable and function names should be all lowercase.**
```r
  diffuse.data$frame$DiffusionEffect <- mrw
                     ^~~~~~~~~~~~~~~
```
[R/inference_diffuse.R:187:58:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse.R#L187) *style:* **Variable and function names should be all lowercase.**
```r
  boot.g <- tidyr::gather(bootstrap.hits, Boot, Effect, -GeneSymbol) %>%
                                                         ^~~~~~~~~~
```
[R/inference_diffuse.R:200:1:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse.R#L200) *style:* **lines should not be more than 80 characters.**
```r
  # -> calculate means -> calculate alphas -> calculate variance -> calculate alpha_0
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference_diffuse.R:206:21:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse.R#L206) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::group_by(GeneSymbol) %>%
                    ^~~~~~~~~~
```
[R/inference_diffuse.R:208:29:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse.R#L208) *style:* **Variable and function names should be all lowercase.**
```r
                       mean(DiffusionEffect, na.rm=T)) %>%
                            ^~~~~~~~~~~~~~~
```
[R/inference_diffuse.R:211:57:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse.R#L211) *style:* **Variable and function names should be all lowercase.**
```r
                          tidyr::spread(flat.dat, boot, DiffusionEffect),
                                                        ^~~~~~~~~~~~~~~
```
[R/inference_diffuse.R:230:56:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse.R#L230) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::filter(Idx %in% as.integer(names(neighs))))$GeneSymbol
                                                       ^~~~~~~~~~
```
[R/inference_diffuse.R:234:21:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse.R#L234) *style:* **Variable and function names should be all lowercase.**
```r
      dplyr::select(GeneSymbol, Effect)}
                    ^~~~~~~~~~
```
[R/inference_diffuse.R:243:49:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_diffuse.R#L243) *style:* **Variable and function names should be all lowercase.**
```r
  genes.found <- dplyr::select(flat.dat, Start, GeneSymbol) %>%
                                                ^~~~~~~~~~
```
[R/inference_gesper.R:60:47:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_gesper.R#L60) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::filter(obj, !is.na(Entrez), !is.na(siRNAIDs)) %>%
                                              ^~~~~~~~
```
[R/inference_gesper.R:66:33:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_gesper.R#L66) *style:* **Variable and function names should be all lowercase.**
```r
    res <- dplyr::group_by(res, GeneSymbol) %>%
                                ^~~~~~~~~~
```
[R/inference_gesper.R:73:10:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_gesper.R#L73) *style:* **Variable and function names should be all lowercase.**
```r
  res <- .gespeR(res, path)
         ^~~~~~~
```
[R/inference_gesper.R:80:1:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_gesper.R#L80) *style:* **Variable and function names should be all lowercase.**
```r
.gespeR <- function(obj, path)
^~~~~~~
```
[R/inference_gesper.R:84:1:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_gesper.R#L84) *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:91:61:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_gesper.R#L91) *style:* **Variable and function names should be all lowercase.**
```r
                               ids=as.character(pheno.frame$siRNAIDs),
                                                            ^~~~~~~~
```
[R/inference_gesper.R:105:45:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_gesper.R#L105) *style:* **Variable and function names should be all lowercase.**
```r
                         dplyr::select(obj, GeneSymbol, Entrez) %>% unique,
                                            ^~~~~~~~~~
```
[R/inference_gesper.R:107:26:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_gesper.R#L107) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::filter(!is.na(GeneSymbol))
                         ^~~~~~~~~~
```
[R/inference_gesper.R:119:26:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_gesper.R#L119) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::select(Virus, GeneSymbol, Entrez, siRNAIDs, Readout) %>%
                         ^~~~~~~~~~
```
[R/inference_gesper.R:119:46:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_gesper.R#L119) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::select(Virus, GeneSymbol, Entrez, siRNAIDs, Readout) %>%
                                             ^~~~~~~~
```
[R/inference_gesper.R:120:13:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_gesper.R#L120) *style:* **Variable and function names should be all lowercase.**
```r
    .[order(siRNAIDs)]
            ^~~~~~~~
```
[R/inference_gesper.R:123:44:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_gesper.R#L123) *style:* **Variable and function names should be all lowercase.**
```r
  pheno.sirnas   <- as.character(pheno.mat$siRNAIDs)
                                           ^~~~~~~~
```
[R/inference_gesper.R:169:48:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_gesper.R#L169) *style:* **Variable and function names should be all lowercase.**
```r
                            siRNAIDs=pheno.mat$siRNAIDs,
                                               ^~~~~~~~
```
[R/inference_gesper.R:176:43:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_gesper.R#L176) *style:* **Variable and function names should be all lowercase.**
```r
  assertthat::assert_that(all(pheno.frame$siRNAIDs == rel.mat@siRNAs))
                                          ^~~~~~~~
```
[R/inference_gesper.R:177:43:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_gesper.R#L177) *style:* **Variable and function names should be all lowercase.**
```r
  assertthat::assert_that(all(pheno.frame$siRNAIDs ==
                                          ^~~~~~~~
```
[R/inference_gesper.R:191:50:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_gesper.R#L191) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::mutate(siRNAIDs=strsplit(as.character(siRNAIDs), ",")) %>%
                                                 ^~~~~~~~
```
[R/inference_gesper.R:192:19:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_gesper.R#L192) *style:* **Variable and function names should be all lowercase.**
```r
    tidyr::unnest(siRNAIDs)
                  ^~~~~~~~
```
[R/inference_gesper.R:208:1:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_gesper.R#L208) *style:* **Variable and function names should be all lowercase.**
```r
.prioritize.gespeR <- function(obj,
^~~~~~~~~~~~~~~~~~
```
[R/inference_hyperstatistic.R:100:59:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L100) *style:* **Variable and function names should be all lowercase.**
```r
  grp.indexes <- dplyr::group_indices(obj, Virus, Screen, ReadoutType,
                                                          ^~~~~~~~~~~
```
[R/inference_hyperstatistic.R:101:39:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L101) *style:* **Variable and function names should be all lowercase.**
```r
                                      ScreenType, Library, Design, Cell)
                                      ^~~~~~~~~~
```
[R/inference_hyperstatistic.R:114:52:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L114) *style:* **Variable and function names should be all lowercase.**
```r
                                           grp.dat$ScreenType[1],
                                                   ^~~~~~~~~~
```
[R/inference_hyperstatistic.R:115:52:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L115) *style:* **Variable and function names should be all lowercase.**
```r
                                           grp.dat$ReadoutType[1],
                                                   ^~~~~~~~~~~
```
[R/inference_hyperstatistic.R:145:28:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L145) *style:* **Variable and function names should be all lowercase.**
```r
                           ScreenType, ReadoutType,
                           ^~~~~~~~~~
```
[R/inference_hyperstatistic.R:145:40:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L145) *style:* **Variable and function names should be all lowercase.**
```r
                           ScreenType, ReadoutType,
                                       ^~~~~~~~~~~
```
[R/inference_hyperstatistic.R:147:35:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L147) *style:* **Variable and function names should be all lowercase.**
```r
                           Plate, RowIdx, ColIdx,
                                  ^~~~~~
```
[R/inference_hyperstatistic.R:147:43:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L147) *style:* **Variable and function names should be all lowercase.**
```r
                           Plate, RowIdx, ColIdx,
                                          ^~~~~~
```
[R/inference_hyperstatistic.R:148:28:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L148) *style:* **Variable and function names should be all lowercase.**
```r
                           GeneSymbol, Entrez, siRNAIDs) %>%
                           ^~~~~~~~~~
```
[R/inference_hyperstatistic.R:148:48:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L148) *style:* **Variable and function names should be all lowercase.**
```r
                           GeneSymbol, Entrez, siRNAIDs) %>%
                                               ^~~~~~~~
```
[R/inference_hyperstatistic.R:162:55:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L162) *style:* **Variable and function names should be all lowercase.**
```r
  res <- dplyr::group_by(res, Virus, Screen, Library, ReadoutType, ScreenType,
                                                      ^~~~~~~~~~~
```
[R/inference_hyperstatistic.R:162:68:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L162) *style:* **Variable and function names should be all lowercase.**
```r
  res <- dplyr::group_by(res, Virus, Screen, Library, ReadoutType, ScreenType,
                                                                   ^~~~~~~~~~
```
[R/inference_hyperstatistic.R:164:35:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L164) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::mutate(HRes=.hypertest(GeneSymbol, siRNAIDs, Plate,
                                  ^~~~~~~~~~
```
[R/inference_hyperstatistic.R:164:47:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L164) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::mutate(HRes=.hypertest(GeneSymbol, siRNAIDs, Plate,
                                              ^~~~~~~~
```
[R/inference_hyperstatistic.R:165:35:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L165) *style:* **Variable and function names should be all lowercase.**
```r
                                  RowIdx, ColIdx, Readout, level)) %>%
                                  ^~~~~~
```
[R/inference_hyperstatistic.R:165:43:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L165) *style:* **Variable and function names should be all lowercase.**
```r
                                  RowIdx, ColIdx, Readout, level)) %>%
                                          ^~~~~~
```
[R/inference_hyperstatistic.R:175:27:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L175) *style:* **Variable and function names should be all lowercase.**
```r
  data.table::setDT(res)[,HyperRank := cumsum(res$Hit)]
                          ^~~~~~~~~
```
[R/inference_hyperstatistic.R:176:36:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L176) *style:* **Variable and function names should be all lowercase.**
```r
  data.table::setDT(res)[Hit == 0, HyperRank := NA_integer_]
                                   ^~~~~~~~~
```
[R/inference_hyperstatistic.R:197:1:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L197) *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:254:26:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L254) *style:* **Variable and function names should be all lowercase.**
```r
                         ScreenType, ReadoutType,
                         ^~~~~~~~~~
```
[R/inference_hyperstatistic.R:254:38:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L254) *style:* **Variable and function names should be all lowercase.**
```r
                         ScreenType, ReadoutType,
                                     ^~~~~~~~~~~
```
[R/inference_hyperstatistic.R:256:26:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L256) *style:* **Variable and function names should be all lowercase.**
```r
                         GeneSymbol, Entrez) %>%
                         ^~~~~~~~~~
```
[R/inference_hyperstatistic.R:268:19:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_hyperstatistic.R#L268) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::filter(HitRatio >= hit.ratio)
                  ^~~~~~~~
```
[R/inference_lmm_fdr_ge.R:37:62:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_ge.R#L37) *style:* **Variable and function names should be all lowercase.**
```r
    dt <- data.table::data.table(GeneSymbol=ref$gene.effects$GeneSymbol,
                                                             ^~~~~~~~~~
```
[R/inference_lmm_fdr_ge.R:59:38:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_ge.R#L59) *style:* **Variable and function names should be all lowercase.**
```r
        GeneSymbol = re$gene.effects$GeneSymbol
                                     ^~~~~~~~~~
```
[R/inference_lmm_fdr_ge.R:90:31:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_ge.R#L90) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::group_by(btst.dat, GeneSymbol) %>%
                              ^~~~~~~~~~
```
[R/inference_lmm_fdr_gpe.R:89:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L89) *style:* **Use <-, not =, for assignment.**
```r
  call = match.call()
       ^
```
[R/inference_lmm_fdr_gpe.R:106:13:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L106) *style:* **Use <-, not =, for assignment.**
```r
        med = median(zz)
            ^
```
[R/inference_lmm_fdr_gpe.R:107:12:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L107) *style:* **Use <-, not =, for assignment.**
```r
        ra = med + (1 - pct) * (range(zz) - med)
           ^
```
[R/inference_lmm_fdr_gpe.R:108:12:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L108) *style:* **Use <-, not =, for assignment.**
```r
        lo = ra[1]
           ^
```
[R/inference_lmm_fdr_gpe.R:109:12:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L109) *style:* **Use <-, not =, for assignment.**
```r
        up = ra[2]
           ^
```
[R/inference_lmm_fdr_gpe.R:146:9:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L146) *style:* **Use <-, not =, for assignment.**
```r
    fp0 = matrix(NA, 6, 4)
        ^
```
[R/inference_lmm_fdr_gpe.R:147:19:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L147) *style:* **Use <-, not =, for assignment.**
```r
    colnames(fp0) = c("delta", "sigleft", "p0", "sigright")
                  ^
```
[R/inference_lmm_fdr_gpe.R:150:9:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L150) *style:* **Use <-, not =, for assignment.**
```r
    fp0 = matrix(NA, 6, 3)
        ^
```
[R/inference_lmm_fdr_gpe.R:151:19:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L151) *style:* **Use <-, not =, for assignment.**
```r
    colnames(fp0) = c("delta", "sigma", "p0")
                  ^
```
[R/inference_lmm_fdr_gpe.R:153:17:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L153) *style:* **Use <-, not =, for assignment.**
```r
  rownames(fp0) = c("thest", "theSD", "mlest", "mleSD", "cmest",  "cmeSD")
                ^
```
[R/inference_lmm_fdr_gpe.R:154:21:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L154) *style:* **Use <-, not =, for assignment.**
```r
  fp0["thest", 1:2] = c(0, 1)
                    ^
```
[R/inference_lmm_fdr_gpe.R:155:21:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L155) *style:* **Use <-, not =, for assignment.**
```r
  fp0["theSD", 1:2] = 0
                    ^
```
[R/inference_lmm_fdr_gpe.R:181:13:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L181) *style:* **Use <-, not =, for assignment.**
```r
    cmerror = I(is.na(co[3]) | is.na(co[2]))
            ^
```
[R/inference_lmm_fdr_gpe.R:183:15:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L183) *style:* **Use <-, not =, for assignment.**
```r
      cmerror = I(co[2] >= 0 | co[2] + co[3] >= 0)
              ^
```
[R/inference_lmm_fdr_gpe.R:186:13:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L186) *style:* **Use <-, not =, for assignment.**
```r
    cmerror = is.na(co[3])
            ^
```
[R/inference_lmm_fdr_gpe.R:188:15:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L188) *style:* **Use <-, not =, for assignment.**
```r
      cmerror = I(co[3] >= 0)
              ^
```
[R/inference_lmm_fdr_gpe.R:218:5:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L218) *style:* **Use <-, not =, for assignment.**
```r
  b = 4.3 * exp(-0.26 * log(N, 10))
    ^
```
[R/inference_lmm_fdr_gpe.R:220:9:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L220) *style:* **Use <-, not =, for assignment.**
```r
    med = median(zz)
        ^
```
[R/inference_lmm_fdr_gpe.R:221:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L221) *style:* **Use <-, not =, for assignment.**
```r
    sc = diff(quantile(zz)[c(2, 4)])/(2 * stats::qnorm(0.75))
       ^
```
[R/inference_lmm_fdr_gpe.R:222:12:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L222) *style:* **Use <-, not =, for assignment.**
```r
    mlests = locmle(zz, xlim = c(med, b * sc))
           ^
```
[R/inference_lmm_fdr_gpe.R:224:1:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L224) *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_fdr_gpe.R:226:14:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L226) *style:* **Use <-, not =, for assignment.**
```r
      mlests = locmle(zz, xlim = c(med, sc))
             ^
```
[R/inference_lmm_fdr_gpe.R:231:9:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L231) *style:* **Use <-, not =, for assignment.**
```r
      b = 1
        ^
```
[R/inference_lmm_fdr_gpe.R:233:14:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L233) *style:* **Use <-, not =, for assignment.**
```r
      Cov.in = list(x = x, X = X, f = f, sw = sw)
             ^
```
[R/inference_lmm_fdr_gpe.R:234:14:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L234) *style:* **Use <-, not =, for assignment.**
```r
      ml.out = locmle(zz, xlim = c(mlests[1], b * mlests[2]),
             ^
```
[R/inference_lmm_fdr_gpe.R:236:14:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L236) *style:* **Use <-, not =, for assignment.**
```r
      mlests = ml.out$mle
             ^
```
[R/inference_lmm_fdr_gpe.R:238:17:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L238) *style:* **Use <-, not =, for assignment.**
```r
    else mlests = locmle(zz, xlim = c(mlests[1], b * mlests[2]),
                ^
```
[R/inference_lmm_fdr_gpe.R:240:23:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L240) *style:* **Use <-, not =, for assignment.**
```r
    fp0["mlest", 1:3] = mlests[1:3]
                      ^
```
[R/inference_lmm_fdr_gpe.R:241:23:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L241) *style:* **Use <-, not =, for assignment.**
```r
    fp0["mleSD", 1:3] = mlests[4:6]
                      ^
```
[R/inference_lmm_fdr_gpe.R:245:1:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L245) *style:* **lines should not be more than 80 characters.**
```r
                                                              2]/mlests[2])) > 0.05)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference_lmm_fdr_gpe.R:246:1:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L246) *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_fdr_gpe.R:256:12:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L256) *style:* **Use <-, not =, for assignment.**
```r
    delhat = xmax = xmaxx = mlests[1]
           ^
```
[R/inference_lmm_fdr_gpe.R:256:19:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L256) *style:* **Use <-, not =, for assignment.**
```r
    delhat = xmax = xmaxx = mlests[1]
                  ^
```
[R/inference_lmm_fdr_gpe.R:256:27:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L256) *style:* **Use <-, not =, for assignment.**
```r
    delhat = xmax = xmaxx = mlests[1]
                          ^
```
[R/inference_lmm_fdr_gpe.R:257:12:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L257) *style:* **Use <-, not =, for assignment.**
```r
    sighat = mlests[2]
           ^
```
[R/inference_lmm_fdr_gpe.R:258:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L258) *style:* **Use <-, not =, for assignment.**
```r
    p0 = mlests[3]
       ^
```
[R/inference_lmm_fdr_gpe.R:259:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L259) *style:* **Use <-, not =, for assignment.**
```r
    f0 = stats::dnorm(x, delhat, sighat)
       ^
```
[R/inference_lmm_fdr_gpe.R:260:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L260) *style:* **Use <-, not =, for assignment.**
```r
    f0 = (sum(f) * f0)/sum(f0)
       ^
```
[R/inference_lmm_fdr_gpe.R:262:7:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L262) *style:* **Use <-, not =, for assignment.**
```r
  fdr = pmin((p0 * f0)/f, 1)
      ^
```
[R/inference_lmm_fdr_gpe.R:266:19:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L266) *style:* **Use <-, not =, for assignment.**
```r
  fp0["thest", 3] = p0theo
                  ^
```
[R/inference_lmm_fdr_gpe.R:278:13:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L278) *style:* **Use <-, not =, for assignment.**
```r
  else xxlo = xmax
            ^
```
[R/inference_lmm_fdr_gpe.R:281:13:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L281) *style:* **Use <-, not =, for assignment.**
```r
  else xxhi = xmax
            ^
```
[R/inference_lmm_fdr_gpe.R:286:13:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L286) *style:* **Use <-, not =, for assignment.**
```r
  else xxlo = xmax
            ^
```
[R/inference_lmm_fdr_gpe.R:289:13:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L289) *style:* **Use <-, not =, for assignment.**
```r
  else xxhi = xmax
            ^
```
[R/inference_lmm_fdr_gpe.R:293:66:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L293) *style:* **Use <-, not =, for assignment.**
```r
    fdr[x >= mlests[1] - mlests[2] & x <= mlests[1] + mlests[2]] = 1
                                                                 ^
```
[R/inference_lmm_fdr_gpe.R:294:67:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L294) *style:* **Use <-, not =, for assignment.**
```r
    fdr0[x >= mlests[1] - mlests[2] & x <= mlests[1] + mlests[2]] = 1
                                                                  ^
```
[R/inference_lmm_fdr_gpe.R:305:1:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L305) *style:* **lines should not be more than 80 characters.**
```r
                                                             fdr[ido]) * fall[ido])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference_lmm_fdr_gpe.R:307:1:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L307) *style:* **lines should not be more than 80 characters.**
```r
                                                                fdr0[ido]) * fall[ido])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference_lmm_fdr_gpe.R:309:1:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L309) *style:* **lines should not be more than 80 characters.**
```r
                                                              fdr[iup]) * fall[iup])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference_lmm_fdr_gpe.R:311:1:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L311) *style:* **lines should not be more than 80 characters.**
```r
                                                                 fdr0[iup]) * fall[iup])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/inference_lmm_fdr_gpe.R:313:28:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L313) *style:* **Use <-, not =, for assignment.**
```r
  Efdr[which(is.na(Efdr))] = 1
                           ^
```
[R/inference_lmm_fdr_gpe.R:320:9:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L320) *style:* **Use <-, not =, for assignment.**
```r
    mul = c(1, mult)
        ^
```
[R/inference_lmm_fdr_gpe.R:321:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L321) *style:* **Use <-, not =, for assignment.**
```r
    EE = rep(0, length(mul))
       ^
```
[R/inference_lmm_fdr_gpe.R:323:10:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L323) *style:* **Use <-, not =, for assignment.**
```r
      xe = sqrt(mul[m]) * x
         ^
```
[R/inference_lmm_fdr_gpe.R:324:11:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L324) *style:* **Use <-, not =, for assignment.**
```r
      f1e = approx(xe, f1, x, rule = 2, ties = mean)$y
          ^
```
[R/inference_lmm_fdr_gpe.R:325:11:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L325) *style:* **Use <-, not =, for assignment.**
```r
      f1e = (f1e * sum(f1))/sum(f1e)
          ^
```
[R/inference_lmm_fdr_gpe.R:326:11:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L326) *style:* **Use <-, not =, for assignment.**
```r
      f0e = f0
          ^
```
[R/inference_lmm_fdr_gpe.R:327:11:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L327) *style:* **Use <-, not =, for assignment.**
```r
      p0e = p0
          ^
```
[R/inference_lmm_fdr_gpe.R:329:13:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L329) *style:* **Use <-, not =, for assignment.**
```r
        f0e = f00
            ^
```
[R/inference_lmm_fdr_gpe.R:330:13:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L330) *style:* **Use <-, not =, for assignment.**
```r
        p0e = p0theo
            ^
```
[R/inference_lmm_fdr_gpe.R:332:12:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L332) *style:* **Use <-, not =, for assignment.**
```r
      fdre = (p0e * f0e)/(p0e * f0e + f1e)
           ^
```
[R/inference_lmm_fdr_gpe.R:333:13:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L333) *style:* **Use <-, not =, for assignment.**
```r
      EE[m] = sum(f1e * fdre)/sum(f1e)
            ^
```
[R/inference_lmm_fdr_gpe.R:335:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L335) *style:* **Use <-, not =, for assignment.**
```r
    EE = EE/EE[1]
       ^
```
[R/inference_lmm_fdr_gpe.R:336:15:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L336) *style:* **Use <-, not =, for assignment.**
```r
    names(EE) = mul
              ^
```
[R/inference_lmm_fdr_gpe.R:338:12:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L338) *style:* **Use <-, not =, for assignment.**
```r
  Cov2.out = loccov2(X, X0, i0, f, fp0["cmest", ], N)
           ^
```
[R/inference_lmm_fdr_gpe.R:339:12:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L339) *style:* **Use <-, not =, for assignment.**
```r
  Cov0.out = loccov2(X, matrix(1, length(x), 1), i0, f, fp0["thest",
           ^
```
[R/inference_lmm_fdr_gpe.R:343:13:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L343) *style:* **Use <-, not =, for assignment.**
```r
      Ilfdr = Cov0.out$Ilfdr
            ^
```
[R/inference_lmm_fdr_gpe.R:345:13:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L345) *style:* **Use <-, not =, for assignment.**
```r
      Ilfdr = ml.out$Ilfdr
            ^
```
[R/inference_lmm_fdr_gpe.R:347:13:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L347) *style:* **Use <-, not =, for assignment.**
```r
      Ilfdr = Cov2.out$Ilfdr
            ^
```
[R/inference_lmm_fdr_gpe.R:352:9:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L352) *style:* **Use <-, not =, for assignment.**
```r
    Cov = Cov0.out$Cov
        ^
```
[R/inference_lmm_fdr_gpe.R:354:9:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L354) *style:* **Use <-, not =, for assignment.**
```r
    Cov = ml.out$Cov.lfdr
        ^
```
[R/inference_lmm_fdr_gpe.R:355:12:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L355) *style:* **Use <-, not =, for assignment.**
```r
  else Cov = Cov2.out$Cov
           ^
```
[R/inference_lmm_fdr_gpe.R:357:21:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L357) *style:* **Use <-, not =, for assignment.**
```r
  fp0["cmeSD", 1:3] = Cov2.out$stdev[c(2, 3, 1)]
                    ^
```
[R/inference_lmm_fdr_gpe.R:359:21:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L359) *style:* **Use <-, not =, for assignment.**
```r
    fp0["cmeSD", 4] = fp0["cmeSD", 2]
                    ^
```
[R/inference_lmm_fdr_gpe.R:360:19:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L360) *style:* **Use <-, not =, for assignment.**
```r
  fp0["theSD", 3] = Cov0.out$stdev[1]
                  ^
```
[R/inference_lmm_fdr_gpe.R:363:11:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L363) *style:* **Use <-, not =, for assignment.**
```r
      pds = fp0["thest", c(3, 1, 2)]
          ^
```
[R/inference_lmm_fdr_gpe.R:364:13:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L364) *style:* **Use <-, not =, for assignment.**
```r
      stdev = fp0["theSD", c(3, 1, 2)]
            ^
```
[R/inference_lmm_fdr_gpe.R:365:12:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L365) *style:* **Use <-, not =, for assignment.**
```r
      pds. = t(Cov0.out$pds.)
           ^
```
[R/inference_lmm_fdr_gpe.R:368:11:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L368) *style:* **Use <-, not =, for assignment.**
```r
      pds = fp0["mlest", c(3, 1, 2)]
          ^
```
[R/inference_lmm_fdr_gpe.R:369:13:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L369) *style:* **Use <-, not =, for assignment.**
```r
      stdev = fp0["mleSD", c(3, 1, 2)]
            ^
```
[R/inference_lmm_fdr_gpe.R:370:12:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L370) *style:* **Use <-, not =, for assignment.**
```r
      pds. = t(ml.out$pds.)
           ^
```
[R/inference_lmm_fdr_gpe.R:373:11:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L373) *style:* **Use <-, not =, for assignment.**
```r
      pds = fp0["cmest", c(3, 1, 2)]
          ^
```
[R/inference_lmm_fdr_gpe.R:374:13:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L374) *style:* **Use <-, not =, for assignment.**
```r
      stdev = fp0["cmeSD", c(3, 1, 2)]
            ^
```
[R/inference_lmm_fdr_gpe.R:375:12:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L375) *style:* **Use <-, not =, for assignment.**
```r
      pds. = t(Cov2.out$pds.)
           ^
```
[R/inference_lmm_fdr_gpe.R:378:20:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L378) *style:* **Use <-, not =, for assignment.**
```r
    colnames(pds.) = names(pds) = c("p0", "delhat", "sighat")
                   ^
```
[R/inference_lmm_fdr_gpe.R:378:33:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L378) *style:* **Use <-, not =, for assignment.**
```r
    colnames(pds.) = names(pds) = c("p0", "delhat", "sighat")
                                ^
```
[R/inference_lmm_fdr_gpe.R:379:18:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L379) *style:* **Use <-, not =, for assignment.**
```r
    names(stdev) = c("sdp0", "sddelhat", "sdsighat")
                 ^
```
[R/inference_lmm_fdr_gpe.R:396:7:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L396) *style:* **Use <-, not =, for assignment.**
```r
  z.2 = rep(NA, 2)
      ^
```
[R/inference_lmm_fdr_gpe.R:397:5:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L397) *style:* **Use <-, not =, for assignment.**
```r
  m = order(fd)[nx]
    ^
```
[R/inference_lmm_fdr_gpe.R:399:12:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L399) *style:* **Use <-, not =, for assignment.**
```r
    z.2[2] = stats::approx(fd[m:nx], x[m:nx], 0.2, ties = mean)$y
           ^
```
[R/inference_lmm_fdr_gpe.R:402:12:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L402) *style:* **Use <-, not =, for assignment.**
```r
    z.2[1] = stats::approx(fd[1:m], x[1:m], 0.2, ties = mean)$y
           ^
```
[R/inference_lmm_fdr_gpe.R:416:6:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L416) *style:* **Use <-, not =, for assignment.**
```r
  vl = list(fdr = ffdr, fp0 = fp0, Efdr = Efdr, cdf1 = cdf1,
     ^
```
[R/inference_lmm_fdr_gpe.R:419:13:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L419) *style:* **Use <-, not =, for assignment.**
```r
    vl$mult = EE
            ^
```
[R/inference_lmm_fdr_gpe.R:420:11:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L420) *style:* **Use <-, not =, for assignment.**
```r
  vl$call = call
          ^
```
[R/inference_lmm_fdr_gpe.R:431:5:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L431) *style:* **Use <-, not =, for assignment.**
```r
  N = length(z)
    ^
```
[R/inference_lmm_fdr_gpe.R:434:9:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L434) *style:* **Use <-, not =, for assignment.**
```r
      b = 1
        ^
```
[R/inference_lmm_fdr_gpe.R:435:12:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L435) *style:* **Use <-, not =, for assignment.**
```r
    else b = 4.3 * exp(-0.26 * log(N, 10))
           ^
```
[R/inference_lmm_fdr_gpe.R:436:10:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L436) *style:* **Use <-, not =, for assignment.**
```r
    xlim = c(median(z), b * diff(quantile(z)[c(2, 4)])/(2 *
         ^
```
[R/inference_lmm_fdr_gpe.R:439:9:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L439) *style:* **Use <-, not =, for assignment.**
```r
  aorig = xlim[1] - xlim[2]
        ^
```
[R/inference_lmm_fdr_gpe.R:440:9:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L440) *style:* **Use <-, not =, for assignment.**
```r
  borig = xlim[1] + xlim[2]
        ^
```
[R/inference_lmm_fdr_gpe.R:441:6:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L441) *style:* **Use <-, not =, for assignment.**
```r
  z0 = z[which(z >= aorig & z <= borig)]
     ^
```
[R/inference_lmm_fdr_gpe.R:442:6:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L442) *style:* **Use <-, not =, for assignment.**
```r
  N0 = length(z0)
     ^
```
[R/inference_lmm_fdr_gpe.R:443:5:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L443) *style:* **Use <-, not =, for assignment.**
```r
  Y = c(mean(z0), mean(z0^2))
    ^
```
[R/inference_lmm_fdr_gpe.R:444:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L444) *style:* **Use <-, not =, for assignment.**
```r
  that = N0/N
       ^
```
[R/inference_lmm_fdr_gpe.R:446:9:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L446) *style:* **Use <-, not =, for assignment.**
```r
    bet = c(d/s^2, -1/(2 * s^2))
        ^
```
[R/inference_lmm_fdr_gpe.R:447:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L447) *style:* **Use <-, not =, for assignment.**
```r
    aa = (aorig - d)/s
       ^
```
[R/inference_lmm_fdr_gpe.R:448:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L448) *style:* **Use <-, not =, for assignment.**
```r
    bb = (borig - d)/s
       ^
```
[R/inference_lmm_fdr_gpe.R:449:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L449) *style:* **Use <-, not =, for assignment.**
```r
    H0 = pnorm(bb) - pnorm(aa)
       ^
```
[R/inference_lmm_fdr_gpe.R:450:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L450) *style:* **Use <-, not =, for assignment.**
```r
    fa = dnorm(aa)
       ^
```
[R/inference_lmm_fdr_gpe.R:451:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L451) *style:* **Use <-, not =, for assignment.**
```r
    fb = dnorm(bb)
       ^
```
[R/inference_lmm_fdr_gpe.R:452:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L452) *style:* **Use <-, not =, for assignment.**
```r
    H1 = fa - fb
       ^
```
[R/inference_lmm_fdr_gpe.R:453:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L453) *style:* **Use <-, not =, for assignment.**
```r
    H2 = H0 + aa * fa - bb * fb
       ^
```
[R/inference_lmm_fdr_gpe.R:454:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L454) *style:* **Use <-, not =, for assignment.**
```r
    H3 = (2 + aa^2) * fa - (2 + bb^2) * fb
       ^
```
[R/inference_lmm_fdr_gpe.R:455:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L455) *style:* **Use <-, not =, for assignment.**
```r
    H4 = 3 * H0 + (3 * aa + aa^3) * fa - (3 * bb + bb^3) *
       ^
```
[R/inference_lmm_fdr_gpe.R:457:7:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L457) *style:* **Use <-, not =, for assignment.**
```r
    H = c(H0, H1, H2, H3, H4)
      ^
```
[R/inference_lmm_fdr_gpe.R:458:7:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L458) *style:* **Use <-, not =, for assignment.**
```r
    r = d/s
      ^
```
[R/inference_lmm_fdr_gpe.R:459:7:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L459) *style:* **Use <-, not =, for assignment.**
```r
    I = matrix(rep(0, 25), 5)
      ^
```
[R/inference_lmm_fdr_gpe.R:460:40:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L460) *style:* **Use <-, not =, for assignment.**
```r
    for (i in 0:4) I[i + 1, 0:(i + 1)] = choose(i, 0:i)
                                       ^
```
[R/inference_lmm_fdr_gpe.R:461:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L461) *style:* **Use <-, not =, for assignment.**
```r
    u1 = s^(0:4)
       ^
```
[R/inference_lmm_fdr_gpe.R:462:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L462) *style:* **Use <-, not =, for assignment.**
```r
    II = pmax(row(I) - col(I), 0)
       ^
```
[R/inference_lmm_fdr_gpe.R:463:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L463) *style:* **Use <-, not =, for assignment.**
```r
    II = r^II
       ^
```
[R/inference_lmm_fdr_gpe.R:464:7:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L464) *style:* **Use <-, not =, for assignment.**
```r
    I = u1 * (I * II)
      ^
```
[R/inference_lmm_fdr_gpe.R:465:7:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L465) *style:* **Use <-, not =, for assignment.**
```r
    E = as.vector(I %*% H)/H0
      ^
```
[R/inference_lmm_fdr_gpe.R:466:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L466) *style:* **Use <-, not =, for assignment.**
```r
    E1 = E[2]
       ^
```
[R/inference_lmm_fdr_gpe.R:467:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L467) *style:* **Use <-, not =, for assignment.**
```r
    E2 = E[3]
       ^
```
[R/inference_lmm_fdr_gpe.R:468:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L468) *style:* **Use <-, not =, for assignment.**
```r
    E3 = E[4]
       ^
```
[R/inference_lmm_fdr_gpe.R:469:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L469) *style:* **Use <-, not =, for assignment.**
```r
    E4 = E[5]
       ^
```
[R/inference_lmm_fdr_gpe.R:470:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L470) *style:* **Use <-, not =, for assignment.**
```r
    mu = c(E1, E2)
       ^
```
[R/inference_lmm_fdr_gpe.R:471:7:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L471) *style:* **Use <-, not =, for assignment.**
```r
    V = matrix(c(E2 - E1^2, E3 - E1 * E2, E3 - E1 * E2, E4 -
      ^
```
[R/inference_lmm_fdr_gpe.R:473:10:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L473) *style:* **Use <-, not =, for assignment.**
```r
    bett = bet + solve(V, Y - mu)/(1 + 1/j^2)
         ^
```
[R/inference_lmm_fdr_gpe.R:475:12:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L475) *style:* **Use <-, not =, for assignment.**
```r
      bett = bet + 0.1 * solve(V, Y - mu)/(1 + 1/j^2)
           ^
```
[R/inference_lmm_fdr_gpe.R:480:7:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L480) *style:* **Use <-, not =, for assignment.**
```r
    d = -bett[1]/(2 * bett[2])
      ^
```
[R/inference_lmm_fdr_gpe.R:481:7:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L481) *style:* **Use <-, not =, for assignment.**
```r
    s = 1/sqrt(-2 * bett[2])
      ^
```
[R/inference_lmm_fdr_gpe.R:486:9:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L486) *style:* **Use <-, not =, for assignment.**
```r
    mle = rep(NA, 6)
        ^
```
[R/inference_lmm_fdr_gpe.R:487:14:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L487) *style:* **Use <-, not =, for assignment.**
```r
    Cov.lfdr = NA
             ^
```
[R/inference_lmm_fdr_gpe.R:488:9:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L488) *style:* **Use <-, not =, for assignment.**
```r
    Cor = matrix(NA, 3, 3)
        ^
```
[R/inference_lmm_fdr_gpe.R:491:9:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L491) *style:* **Use <-, not =, for assignment.**
```r
    mle = rep(NA, 6)
        ^
```
[R/inference_lmm_fdr_gpe.R:492:14:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L492) *style:* **Use <-, not =, for assignment.**
```r
    Cov.lfdr = Cov.out = NA
             ^
```
[R/inference_lmm_fdr_gpe.R:492:24:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L492) *style:* **Use <-, not =, for assignment.**
```r
    Cov.lfdr = Cov.out = NA
                       ^
```
[R/inference_lmm_fdr_gpe.R:493:9:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L493) *style:* **Use <-, not =, for assignment.**
```r
    Cor = matrix(NA, 3, 3)
        ^
```
[R/inference_lmm_fdr_gpe.R:496:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L496) *style:* **Use <-, not =, for assignment.**
```r
    aa = (aorig - d)/s
       ^
```
[R/inference_lmm_fdr_gpe.R:497:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L497) *style:* **Use <-, not =, for assignment.**
```r
    bb = (borig - d)/s
       ^
```
[R/inference_lmm_fdr_gpe.R:498:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L498) *style:* **Use <-, not =, for assignment.**
```r
    H0 = pnorm(bb) - pnorm(aa)
       ^
```
[R/inference_lmm_fdr_gpe.R:499:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L499) *style:* **Use <-, not =, for assignment.**
```r
    p0 = that/H0
       ^
```
[R/inference_lmm_fdr_gpe.R:500:7:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L500) *style:* **Use <-, not =, for assignment.**
```r
    J = s^2 * matrix(c(1, 0, 2 * d, s), 2)
      ^
```
[R/inference_lmm_fdr_gpe.R:501:8:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L501) *style:* **Use <-, not =, for assignment.**
```r
    JV = J %*% solve(V)
       ^
```
[R/inference_lmm_fdr_gpe.R:502:9:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L502) *style:* **Use <-, not =, for assignment.**
```r
    JVJ = JV %*% t(J)
        ^
```
[R/inference_lmm_fdr_gpe.R:503:10:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L503) *style:* **Use <-, not =, for assignment.**
```r
    mat2 = cbind(0, JVJ/N0)
         ^
```
[R/inference_lmm_fdr_gpe.R:504:10:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L504) *style:* **Use <-, not =, for assignment.**
```r
    mat1 = c((p0 * H0 * (1 - p0 * H0))/N, 0, 0)
         ^
```
[R/inference_lmm_fdr_gpe.R:505:9:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L505) *style:* **Use <-, not =, for assignment.**
```r
    mat = rbind(mat1, mat2)
        ^
```
[R/inference_lmm_fdr_gpe.R:506:7:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L506) *style:* **Use <-, not =, for assignment.**
```r
    h = c(H1/H0, (H2 - H0)/H0)
      ^
```
[R/inference_lmm_fdr_gpe.R:507:10:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L507) *style:* **Use <-, not =, for assignment.**
```r
    matt = c(1/H0, -(p0/s) * t(h))
         ^
```
[R/inference_lmm_fdr_gpe.R:508:10:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L508) *style:* **Use <-, not =, for assignment.**
```r
    matt = rbind(matt, cbind(0, diag(2)))
         ^
```
[R/inference_lmm_fdr_gpe.R:509:7:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L509) *style:* **Use <-, not =, for assignment.**
```r
    C = matt %*% (mat %*% t(matt))
      ^
```
[R/inference_lmm_fdr_gpe.R:510:9:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L510) *style:* **Use <-, not =, for assignment.**
```r
    mle = c(p0, d, s, diag(C)^0.5)
        ^
```
[R/inference_lmm_fdr_gpe.R:512:10:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L512) *style:* **Use <-, not =, for assignment.**
```r
      sd = mle[4:6]
         ^
```
[R/inference_lmm_fdr_gpe.R:513:10:](https://github.com/dirmeier/knockout/blob/985ae61c6c7521b7441fc5bc02b0ddeae224a959/R/inference_lmm_fdr_gpe.R#L513) *style:* **Use <-, not =, for assignment.**
```r
      Co = C/outer(sd, sd)
         ^
```


With @TheAkbar


Hi  @tomverin ,

Apologies in advance if this is irrelevant or not the right place or way to do this and causes any inconvenience.

I am currently looking for a Java application / library that can convert an EBCDIC formatted file (from Mainframe) into standard ASCII format. I came across this code base [ebcdic-to-ascii-converter
] and found it really interesting. I was wondering if this application also handles packed / compressed fields (COMP-3) conversion and copybooks?

Awaiting a prompt response.

Thanks in advance.

Kind Regards,
Harish


The code replaces the first 4 characters of the URL with `realm`, so `https://foo/` becomes `realms://foo/`.


Yup. Since this header is now pulled in from another target (the tests target), the header must be namespaced. In general the guideline is that headers imported from other headers need to be namespaced.


thanks for including this :D


thank you