bug fix: use read.delim instead of read_tsv to avoid NA chromosome co…

…lumn (X <- NA)
waldronlab · Sep 2, 2020 · 80fc587 · 80fc587
1 parent 3c8c85d
commit 80fc587
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/R/cBioDataPack.R b/R/cBioDataPack.R
@@ -269,9 +269,9 @@ loadStudy <-
     exptlist <- lapply(expseq, function(i, files, xpnames) {
         fname <- files[[i]]
         message(paste0("Working on: ", fname))
-        dat <- as.data.frame(
-            readr::read_tsv(fname, comment = "#"),
-            check.names = FALSE)
+        dat <- read.delim(
+            fname, sep = "\t", comment.char = "#", stringsAsFactors = FALSE
+        )
         dat <- .cleanHugo(dat)
         dat <- .cleanStrands(dat)
         dat <- .standardizeBuilds(dat)