Style code (GHA)

bigomics · Oct 29, 2024 · 41484cf · 41484cf
1 parent cfd567e
commit 41484cf
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Showing 3 changed files with 37 additions and 37 deletions.
diff --git a/R/pgx-annot.R b/R/pgx-annot.R
@@ -234,9 +234,9 @@ getGeneAnnotation.ANNOTHUB <- function(
   cols <- intersect(cols, AnnotationDbi::keytypes(orgdb))
 
   if (organism %in% c("Mus musculus", "Rattus norvegicus")) {
-      cols <- unique(c(cols, "ENTREZID"))
+    cols <- unique(c(cols, "ENTREZID"))
   }
-  
+
   cat("get gene annotation columns:", cols, "\n")
   message("retrieving annotation for ", length(probes), " ", probe_type, " features...")
 
@@ -251,25 +251,25 @@ getGeneAnnotation.ANNOTHUB <- function(
 
   ## Attempt to retrieve chr map via org.Mm.egCHRLOC / org.Rn.egCHRLOC.
   if (organism %in% c("Mus musculus", "Rattus norvegicus")) {
-      if (organism == "Mus musculus") {
-          library(org.Mm.eg.db)
-          chrloc <- org.Mm.egCHRLOC
-      }
-      if (organism == "Rattus norvegicus") {
-          library(org.Rn.eg.db)
-          chrloc <- org.Rn.egCHRLOC
-      }
-      mapped_genes <- as.list(chrloc[mappedkeys(chrloc)])
-      cm <- intersect(as.character(annot$ENTREZID), names(mapped_genes))
-      mapped_genes <- mapped_genes[cm]
-      locs <- unlist(lapply(mapped_genes, function(x) names(x[1])))
-      jj <- match(names(locs), annot$ENTREZID)
-      annot$MAP <- NA
-      annot$MAP[jj] <- unname(locs)
-      cls <- setdiff(colnames(annot), "ENTREZID")
-      annot <- annot[, cls, drop = FALSE]
-  }
-  
+    if (organism == "Mus musculus") {
+      library(org.Mm.eg.db)
+      chrloc <- org.Mm.egCHRLOC
+    }
+    if (organism == "Rattus norvegicus") {
+      library(org.Rn.eg.db)
+      chrloc <- org.Rn.egCHRLOC
+    }
+    mapped_genes <- as.list(chrloc[mappedkeys(chrloc)])
+    cm <- intersect(as.character(annot$ENTREZID), names(mapped_genes))
+    mapped_genes <- mapped_genes[cm]
+    locs <- unlist(lapply(mapped_genes, function(x) names(x[1])))
+    jj <- match(names(locs), annot$ENTREZID)
+    annot$MAP <- NA
+    annot$MAP[jj] <- unname(locs)
+    cls <- setdiff(colnames(annot), "ENTREZID")
+    annot <- annot[, cls, drop = FALSE]
+  }
+
   # some organisms do not provide symbol but rather gene name (e.g. yeast)
   if (!"SYMBOL" %in% colnames(annot)) {
     annot$SYMBOL <- annot$GENENAME

diff --git a/R/pgx-correlation.R b/R/pgx-correlation.R
@@ -430,20 +430,20 @@ pgx.testPhenoCorrelation <- function(df, plot = TRUE, cex = 1, compute.pv = TRUE
     fisher.P <- NULL
     if (ncol(dd)) {
       fisher.P <- matrix(NA, ncol(dd), ncol(dd))
-      if(nrow(fisher.P) == 1 && ncol(fisher.P) == 1) {
-          tb <- table(dd[, 1], dd[, 1])
-          fisher.P[1, 1] <- stats::fisher.test(tb, simulate.p.value = TRUE)$p.value
+      if (nrow(fisher.P) == 1 && ncol(fisher.P) == 1) {
+        tb <- table(dd[, 1], dd[, 1])
+        fisher.P[1, 1] <- stats::fisher.test(tb, simulate.p.value = TRUE)$p.value
       } else {
-          i <- 1
-          j <- 2
-          for (i in 1:(ncol(dd) - 1)) {
-              kk <- which(!is.na(dd[, i]) & !is.na(dd[, j]))
-              if (length(unique(dd[kk, i])) < 2 || length(unique(dd[kk, j])) < 2) next
-              for (j in (i + 1):ncol(dd)) {
-                  tb <- table(dd[, i], dd[, j])
-                  fisher.P[i, j] <- stats::fisher.test(tb, simulate.p.value = TRUE)$p.value
-              }
+        i <- 1
+        j <- 2
+        for (i in 1:(ncol(dd) - 1)) {
+          kk <- which(!is.na(dd[, i]) & !is.na(dd[, j]))
+          if (length(unique(dd[kk, i])) < 2 || length(unique(dd[kk, j])) < 2) next
+          for (j in (i + 1):ncol(dd)) {
+            tb <- table(dd[, i], dd[, j])
+            fisher.P[i, j] <- stats::fisher.test(tb, simulate.p.value = TRUE)$p.value
           }
+        }
       }
       rownames(fisher.P) <- colnames(dd)
       colnames(fisher.P) <- colnames(dd)

diff --git a/R/pgx-pcsf.R b/R/pgx-pcsf.R
@@ -22,8 +22,8 @@ pgx.computePCSF <- function(pgx, contrast, level = "gene",
     }
     fx <- F[, contrast]
     if (level == "gene") {
-      ##names(fx) <- pgx$genes[rownames(F), "human_ortholog"]
-      fx <- collapse_by_humansymbol(fx, pgx$genes)  ## safe
+      ## names(fx) <- pgx$genes[rownames(F), "human_ortholog"]
+      fx <- collapse_by_humansymbol(fx, pgx$genes) ## safe
     }
   }
 
@@ -62,8 +62,8 @@ pgx.computePCSF <- function(pgx, contrast, level = "gene",
       sel <- (STRING$from %in% nodes & STRING$to %in% nodes)
       ee <- STRING[which(sel), ]
       if (use.corweight) {
-        ##X <- rename_by(pgx$X, pgx$genes, "human_ortholog", unique = TRUE)
-        X <- collapse_by_humansymbol(pgx$X, pgx$genes)  ## safe        
+        ## X <- rename_by(pgx$X, pgx$genes, "human_ortholog", unique = TRUE)
+        X <- collapse_by_humansymbol(pgx$X, pgx$genes) ## safe
         selx <- rownames(X) %in% union(ee$from, ee$to)
         R <- cor(t(X[selx, , drop = FALSE]))
         if (rm.negedge) R[which(R < 0)] <- NA