Merge branch 'main' of https://github.com/bigomics/playbase

bigomics · Nov 13, 2024 · d3dbc3f · d3dbc3f
2 parents fbae691 + 171de70
commit d3dbc3f
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/R/pgx-normalize.R b/R/pgx-normalize.R
@@ -208,7 +208,7 @@ pgx.countNormalization <- function(x, methods, ref = NULL, rm.zero = FALSE) {
     } else if (m == "CPM") {
       x <- logCPM(x, log = FALSE)
     } else if (m == "CP10K") {
-      x <- logCPM(x, total=1e4, log = FALSE)
+      x <- logCPM(x, total = 1e4, log = FALSE)
     } else if (m == "TMM") {
       ## normalization on total counts (linear scale)
       x <- normalizeTMM(x, log = FALSE) ## does TMM on counts (edgeR)

diff --git a/R/pgx-read.R b/R/pgx-read.R
@@ -56,8 +56,8 @@ read.as_matrix <- function(file, skip_row_check = FALSE, as.char = TRUE,
   #      "val1   val2"
   # where columns are read ok by fread
   # but first and last column maintain the "
-  first_column <- x0[[1]]  # Extract the first column
-  last_column <- x0[[ncol(x0)]]  # Extract the last column
+  first_column <- x0[[1]] # Extract the first column
+  last_column <- x0[[ncol(x0)]] # Extract the last column
   if (all(grepl('^"', first_column)) && all(grepl('"$', last_column))) {
     x0[[1]] <- gsub('^"', "", first_column)
     x0[[ncol(x0)]] <- as.numeric(gsub('"$', "", last_column))