From 239654ada63c9e8ca3ab9ec37b45f471a55a026a Mon Sep 17 00:00:00 2001
From: ivokwee <ivokwee@users.noreply.github.com>
Date: Sat, 24 Aug 2024 23:54:24 +0000
Subject: [PATCH] Style code (GHA)

---
 R/gset-meta.r | 2 +-
 R/pgx-read.R  | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/gset-meta.r b/R/gset-meta.r
index 950f4c36..a30f78bf 100644
--- a/R/gset-meta.r
+++ b/R/gset-meta.r
@@ -479,7 +479,7 @@ gset.fitContrastsWithAllMethods <- function(gmt,
   ## v.3.5.0 we use average relative expression instead of average
   ## expression.
   ng <- Matrix::colSums(G != 0)
-  mX <- X - rowMeans(X, na.rm=TRUE) ## see note above
+  mX <- X - rowMeans(X, na.rm = TRUE) ## see note above
   meta.matrix <- as.matrix(Matrix::t(G != 0) %*% mX) / ng
 
   m[["meta"]] <- meta.matrix
diff --git a/R/pgx-read.R b/R/pgx-read.R
index 43c8bfe9..6f639a56 100644
--- a/R/pgx-read.R
+++ b/R/pgx-read.R
@@ -312,7 +312,7 @@ read_samples <- function(file) {
   is_valid <- validate_samples(df)
   if (!is_valid) {
     message("[read_samples] ERROR: Samples file is not valid.")
-    return(NULL)    
+    return(NULL)
   }
   df <- as.data.frame(df)
   return(df)
@@ -333,7 +333,7 @@ read_contrasts <- function(file) {
   is_valid <- validate_contrasts(df)
   if (!is_valid) {
     message("[read_contrasts] ERROR: Contrasts file is not valid.")
-    return(NULL)        
+    return(NULL)
   }
 
   df
@@ -351,7 +351,7 @@ read_annot <- function(file, unique = TRUE) {
     df <- file
   } else {
     message("[read_annot] ERROR: Annot file is not valid.")
-    return(NULL)        
+    return(NULL)
   }
 
   ## add column title