Merge pull request #17 from LUMC/develop

Develop
LUMC · Feb 3, 2021 · a40f0cc · a40f0cc
2 parents 9c3af94 + 976e06d
commit a40f0cc
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Showing 4 changed files with 14 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,11 @@
+Changelog
+==========
+
+<!--
+Newest changes should be on top.
+-->
+
+version 1.4.2
+---------------------------
++ Remove ordering based on FDR in deTab
++ Add Changelog file
diff --git a/inst/src/markdown/analysisDESeq2.Rmd b/inst/src/markdown/analysisDESeq2.Rmd
@@ -224,7 +224,7 @@ normDge$counts <- normDge$counts[intersect(rownames(deTab), rownames(normDge$cou
 #ORDER deTab TABLE
 deTab <- rename(deTab, "FDR" = "adj.P.Val")
 deOrder <- c("avgLog2CPM", "avgLog2FC", "P.Value", "FDR", "DE")
-deTab <- deTab[order(deTab$FDR),]
+
 if (!is.null(data_annotation)) {
   deTab <- deTab[colnames(deTab)
                  [c(1, match(deOrder, names(deTab)), 2:(ncol(deTab) - 5))]]

diff --git a/inst/src/markdown/analysisEdgeR.Rmd b/inst/src/markdown/analysisEdgeR.Rmd
@@ -215,7 +215,7 @@ deTab <- rename(deTab, "avgLog2CPM" = "logCPM")
 deTab <- rename(deTab, "avgLog2FC" = "logFC")
 deTab <- rename(deTab, "P.Value" = "PValue")
 deOrder <- c("avgLog2CPM", "avgLog2FC", "P.Value", "FDR", "DE")
-deTab <- deTab[order(deTab$FDR),]
+
 if (!is.null(data_annotation)) {
   deTab <- deTab[colnames(deTab)
                  [c(1, match(deOrder, names(deTab)), 2:(ncol(deTab) - 5))]]

diff --git a/inst/src/markdown/analysisLimma.Rmd b/inst/src/markdown/analysisLimma.Rmd
@@ -217,7 +217,7 @@ deTab <- rename(deTab, "avgLog2CPM" = "AveExpr")
 deTab <- rename(deTab, "avgLog2FC" = "logFC")
 deTab <- rename(deTab, "FDR" = "adj.P.Val")
 deOrder <- c("avgLog2CPM", "avgLog2FC", "P.Value", "FDR", "DE")
-deTab <- deTab[order(deTab$FDR),]
+
 if (!is.null(data_annotation)) {
   deTab <- deTab[colnames(deTab)
                  [c(1, match(deOrder, names(deTab)), 2:(ncol(deTab) - 5))]]