readGct correctly handles case with no column annotations

ctlab · Aug 28, 2024 · f45afaf · f45afaf
1 parent eb17a1d
commit f45afaf
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Showing 2 changed files with 10 additions and 5 deletions.
diff --git a/R/gct.R b/R/gct.R
@@ -69,7 +69,8 @@ readGct <- function(gct) {
     rownames(fdata) <- rn
 
 
-    if (ann.col > 0) {
+    # parse pData
+    {
         pdata.raw <- t(fread(gct, skip = 2, nrows = ann.col + 1, header=FALSE,
                    colClasses = "character"))
         pdata <- data.frame(pdata.raw[seq_len(ncol(exp)) + 1 + ann.row,],
@@ -80,9 +81,7 @@ readGct <- function(gct) {
         pdata <- makeAnnotated(pdata)
 
         res <- ExpressionSet(exp, featureData = fdata, phenoData = pdata)
-    } else {
-        res <- ExpressionSet(exp, featureData = fdata)
-    }
+    } 
 
     res
 }
@@ -117,7 +116,7 @@ writeGct <- function(es, file, gzip=FALSE) {
                        nrow(es), ncol(es),
                        ann.row-1, ann.col-1), con)
 
-    if (ann.col == 0 && ann.row == 0) {
+    if (ann.col == 0 || ann.row == 0) {
         stop("There should be at least one row and one column annotation")
     }
 

diff --git a/tests/testthat/test-gct.R b/tests/testthat/test-gct.R
@@ -56,6 +56,12 @@ test_that("writeGct and readGct support id column names", {
     expect_identical(pData(es), pData(es2))
 })
 
+test_that("readGct support emptry annotations", {
+    gctFile <- system.file("extdata/testdata/gct/centers.gct", package="phantasusLite")
+    es <- readGct(gctFile)
+    expect_true(ncol(fData(es)) >= 1)
+    expect_true(ncol(pData(es)) >= 1)
+})
 
 test_that("readGct column indexing works with GSE141540.gct file", {
     gctFile <- system.file("extdata/testdata/gct/GSE141540.gct", package="phantasusLite")