Merge branch 'release-1.1.0'

ocbe-uio · Nov 13, 2020 · 5b2b23a · 5b2b23a
2 parents 0c90899 + 24a3bf1
commit 5b2b23a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: DIscBIO
-Date: 2020-10-06
+Date: 2020-11-13
 Title: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics
-Version: 1.0.1
+Version: 1.1.0
 Authors@R:
 	c(
 		person(
@@ -87,8 +87,5 @@ Collate:
     'VolcanoPlot.R'
     'customConverters.R'
     'datasets.R'
+    'internal-functions-samr-adapted.R'
     'internal-functions.R'
-    'prepExampleDataset.R'
-    'reformatSiggenes.R'
-    'replaceDecimals.R'
-    'samr-adapted.R'
diff --git a/NAMESPACE b/NAMESPACE
@@ -141,4 +141,6 @@ importFrom(stats,var)
 importFrom(tsne,tsne)
 importFrom(utils,capture.output)
 importFrom(utils,download.file)
+importFrom(utils,read.table)
 importFrom(utils,write.csv)
+importFrom(utils,write.table)
diff --git a/R/DIscBIO-classes.R b/R/DIscBIO-classes.R
@@ -154,9 +154,9 @@ setMethod(
         tmpFeats <- rownames(.Object@expdataAll)
         tmpExpdataAll <- .Object@expdataAll
 
-        shortNames <- substr(rownames(tmpExpdataAll), 1, 4)
+        shortNames <- substr(rownames(tmpExpdataAll), 1, 3)
         geneTypes <- factor(
-            c(ENSG = "ENSG", ERCC = "ERCM", ENSG = "ENSM")[shortNames]
+            c(ENS = "ENS", ERC = "ERC")[shortNames]
         )
         expdata <- tmpExpdataAll[which(grepl("^ENS", geneTypes)), ]
         .Object@expdata <- expdata