Style code (GHA)

bigomics · Dec 30, 2024 · 677ef15 · 677ef15
1 parent c58cc47
commit 677ef15
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/R/pgx-contrasts.R b/R/pgx-contrasts.R
@@ -842,7 +842,7 @@ contrasts.convertToLabelMatrix <- function(contrasts, samples) {
     all(apply(contrasts, 2, class) %in% c("integer", "numeric"))
   is.numeric.contrast <- is.numeric.matrix | is.numeric.df
   if (is.numeric.contrast) {
-    has.negpos <- any(contrasts < 0, na.rm=TRUE) && any(contrasts > 0, na.rm=TRUE)
+    has.negpos <- any(contrasts < 0, na.rm = TRUE) && any(contrasts > 0, na.rm = TRUE)
     if (has.negpos) {
       contrasts[contrasts %in% c(NA, "NA", "na", "")] <- 0
       contrasts <- sign(contrasts)

diff --git a/R/pgx-read.R b/R/pgx-read.R
@@ -258,9 +258,9 @@ read_files <- function(dir = ".", pattern = NULL) {
   file2 <- head(grep("sample", ff, value = TRUE), 1)
   file3 <- head(grep("contrast|comparison", ff, value = TRUE), 1)
   counts <- samples <- contrasts <- NULL
-  if (length(file1)) counts <- read_counts(file.path(dir,file1))
-  if (length(file2)) samples <- read_samples(file.path(dir,file2))
-  if (length(file3)) contrasts <- read_contrasts(file.path(dir,file3))
+  if (length(file1)) counts <- read_counts(file.path(dir, file1))
+  if (length(file2)) samples <- read_samples(file.path(dir, file2))
+  if (length(file3)) contrasts <- read_contrasts(file.path(dir, file3))
 
   list(
     counts = counts,