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

bigomics · Oct 20, 2023 · b0930a6 · b0930a6
2 parents 1cb993c + 998ab3e
commit b0930a6
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Showing 2 changed files with 7 additions and 8 deletions.
diff --git a/R/pgx-files.R b/R/pgx-files.R
@@ -672,7 +672,7 @@ pgxinfo.updateDatasetFolder <- function(pgx.dir,
     del <- which(h5.files %in% h5.delete)
     if (length(del)) {
       ##      cn[del] <- paste("[DELETED]", sub(".*\\] ", "", cn[del]))
-      cn[del] <- paste("[DELETED]", cn[del])        
+      cn[del] <- paste("[DELETED]", cn[del])
       rhdf5::h5delete(sigdb.file, "data/colnames")
       rhdf5::h5write(cn, sigdb.file, "data/colnames")
       if (delete.old) {
@@ -826,8 +826,8 @@ pgxinfo.updateDatasetFolder <- function(pgx.dir,
       }
       if (fc.del) {
         del <- which(!cn %in% colnames(allFC))
-##        cn[del] <- paste("[DELETED]", sub(".*\\] ", "", cn[del]))
-        cn[del] <- paste("[DELETED]", cn[del])                
+        ##        cn[del] <- paste("[DELETED]", sub(".*\\] ", "", cn[del]))
+        cn[del] <- paste("[DELETED]", cn[del])
         rhdf5::h5delete(sigdb.file, "data/colnames")
         rhdf5::h5write(cn, sigdb.file, "data/colnames")
         if (delete.old) {
@@ -917,8 +917,8 @@ pgxinfo.delete <- function(pgx.dir, pgxname, purge.h5 = FALSE) {
     h5.files <- sub("[.]pgx$", "", h5.files) ## strip pgx
     del <- which(h5.files == pgxname)
     if (length(del)) {
-##      cn[del] <- paste("[DELETED]", sub(".*\\] ", "", cn[del]))
-      cn[del] <- paste("[DELETED]", cn[del])        
+      ##      cn[del] <- paste("[DELETED]", sub(".*\\] ", "", cn[del]))
+      cn[del] <- paste("[DELETED]", cn[del])
       rhdf5::h5delete(sigdb.file, "data/colnames")
       rhdf5::h5write(cn, sigdb.file, "data/colnames")
     }

diff --git a/R/pgx-signature.R b/R/pgx-signature.R
@@ -34,7 +34,6 @@
 #' @export
 pgx.computeConnectivityScores <- function(pgx, sigdb, ntop = 200, contrasts = NULL,
                                           remove.le = FALSE) {
-
   is.h5ref <- grepl("h5$", sigdb)
   if (!is.h5ref) {
     cat("[pgx.computeConnectivityScores] ERROR: must be H5 formatted file\n")
@@ -50,7 +49,7 @@ pgx.computeConnectivityScores <- function(pgx, sigdb, ntop = 200, contrasts = NU
     return(NULL)
   }
 
-  dbg("[pgx.computeConnectivityScores] computing connectivity scores for sigdb = ",sigdb)    
+  dbg("[pgx.computeConnectivityScores] computing connectivity scores for sigdb = ", sigdb)
   meta <- pgx.getMetaFoldChangeMatrix(pgx, what = "meta")
 
   if (is.null(contrasts)) {
@@ -114,7 +113,7 @@ pgx.correlateSignatureH5 <- function(fc, h5.file, nsig = 100, ntop = 200, nperm
   ## if we have less than 100 genes, we should make smaller GMT sets!
   nsig <- min(100, round(length(fc) / 5))
   sel.idx <- 1:length(cn) ## all
-  sel.idx <- grep("DELETED", cn, invert=TRUE)
+  sel.idx <- grep("DELETED", cn, invert = TRUE)
   idx <- list(1:nsig, sel.idx)
   sig100.up <- rhdf5::h5read(h5.file, "signature/sig100.up", index = idx)
   sig100.dn <- rhdf5::h5read(h5.file, "signature/sig100.dn", index = idx)