Remove restatement of params defaults

pinin4fjords · web-flow · commit 6450fbf515bb · 2024-09-03T15:28:55.000+01:00
diff --git a/bin/deseq2_qc.r b/bin/deseq2_qc.r
@@ -103,10 +103,10 @@ if (min(dim(count.table))<=1)  { # No point if only one sample, or one gene
 }
 if (!opt$vst) {
     vst_name <- "rlog"
-    rld      <- rlog(dds, blind=TRUE)   # blind=TRUE is the default and already implied by design=~1
+    rld      <- rlog(dds)
 } else {
     vst_name <- "vst"
-    rld      <- varianceStabilizingTransformation(dds, blind=TRUE)
+    rld      <- varianceStabilizingTransformation(dds)
 }
 
 assay(dds, vst_name) <- assay(rld)

Original file line number	Diff line number	Diff line change
`@@ -103,10 +103,10 @@ if (min(dim(count.table))<=1) { # No point if only one sample, or one gene`
`103`	`103`	`}`
`104`	`104`	`if (!opt$vst) {`
`105`	`105`	`vst_name <- "rlog"`
`106`		`- rld <- rlog(dds, blind=TRUE) # blind=TRUE is the default and already implied by design=~1`
	`106`	`+ rld <- rlog(dds)`
`107`	`107`	`} else {`
`108`	`108`	`vst_name <- "vst"`
`109`		`- rld <- varianceStabilizingTransformation(dds, blind=TRUE)`
	`109`	`+ rld <- varianceStabilizingTransformation(dds)`
`110`	`110`	`}`
`111`	`111`
`112`	`112`	`assay(dds, vst_name) <- assay(rld)`