use specified column to collapse techn repl, in correct helpers.R

esnaultc · esnaultc · commit efdda24ba034 · 2020-08-20T10:18:59.000-04:00
diff --git a/lib/lcdbwf/R/helpers.R b/lib/lcdbwf/R/helpers.R
@@ -412,7 +412,7 @@ make.dds <- function(design_data, salmon.files=NULL, combine.by=NULL,
     }
 
     if(!is.null(combine.by)){
-        dds <-collapseReplicates(dds, dds$biorep)
+        dds <-collapseReplicates(dds, dds[[combine.by]])
     }
 
     dds <- DESeq(dds, ...)

Original file line number	Diff line number	Diff line change
`@@ -412,7 +412,7 @@ make.dds <- function(design_data, salmon.files=NULL, combine.by=NULL,`
`412`	`412`	`}`
`413`	`413`
`414`	`414`	`if(!is.null(combine.by)){`
`415`		`- dds <-collapseReplicates(dds, dds$biorep)`
	`415`	`+ dds <-collapseReplicates(dds, dds[[combine.by]])`
`416`	`416`	`}`
`417`	`417`
`418`	`418`	`dds <- DESeq(dds, ...)`