Style code (GHA)

bigomics · Jan 15, 2025 · e18f406 · e18f406
1 parent d2488c9
commit e18f406
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Showing 3 changed files with 13 additions and 10 deletions.
diff --git a/R/gset-meta.r b/R/gset-meta.r
@@ -530,7 +530,9 @@ gset.fitContrastsWithLIMMA <- function(gsetX, contr.matrix, design,
     vfit <- limma::lmFit(gsetX, design)
     vfit <- limma::contrasts.fit(vfit, contrasts = contr.matrix)
     ## efit <- limma::eBayes(vfit, trend = trend, robust = TRUE)
-    efit <- try({ limma::eBayes(vfit, trend = trend, robust = TRUE) })
+    efit <- try({
+      limma::eBayes(vfit, trend = trend, robust = TRUE)
+    })
     if ("try-error" %in% class(efit)) {
       efit <- limma::eBayes(vfit, trend = trend, robust = FALSE)
     }

diff --git a/R/pgx-annot.R b/R/pgx-annot.R
@@ -626,19 +626,18 @@ getCustomAnnotation <- function(probes, custom_annot = NULL) {
 #' @export
 probe2symbol <- function(probes, annot_table, query = "symbol",
                          key = NULL, fill_na = FALSE) {
-
   # Prepare inputs
-  annot_table <- cbind( rownames = rownames(annot_table), annot_table )
-  probes1 <- setdiff(probes, c(NA,""))
-  if(is.null(key) || !key %in% colnames(annot_table)) {
+  annot_table <- cbind(rownames = rownames(annot_table), annot_table)
+  probes1 <- setdiff(probes, c(NA, ""))
+  if (is.null(key) || !key %in% colnames(annot_table)) {
     key <- which.max(apply(annot_table, 2, function(a) sum(probes1 %in% a)))
   }
-  if(is.null(key)) {
+  if (is.null(key)) {
     stop("[probe2symbol] FATAL. could not get key column.")
   }
-  
+
   # match query
-  ii <- match( probes, annot_table[,key] )
+  ii <- match(probes, annot_table[, key])
   query_col <- annot_table[ii, query]
 
   # Deal with NA

diff --git a/R/pgx-compute.R b/R/pgx-compute.R
@@ -893,8 +893,10 @@ pgx.add_GMT <- function(pgx, custom.geneset = NULL, max.genesets = 20000) {
 
   # Convert G feature/symbol/human_ortholog to SYMBOL
   rownames(G) <- probe2symbol(
-    rownames(G), pgx$genes, key = "human_ortholog",
-    query = "symbol", fill_na = TRUE)
+    rownames(G), pgx$genes,
+    key = "human_ortholog",
+    query = "symbol", fill_na = TRUE
+  )
 
 
   ## -----------------------------------------------------------