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lcolladotor / derfinder

Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches
http://lcolladotor.github.io/derfinder
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rename "foldChange" => "log2FoldChange" for the column in the output regions #4

Closed mikelove closed 10 years ago

mikelove commented 10 years ago

for example, limma and edgeR give a column "logFC", DESeq gives "log2FoldChange"

                ## Calculate fold coverage vs group 1
                if(length(regionGroupMean) > 1){
                        foldChange <- vector("list", length(regionGroupMean) - 1)
                        names(foldChange) <- names(regionGroupMean)[-1]
                        for(group in names(foldChange)) {
                                foldChange[[group]] <- log2(regionGroupMean[[group]] / regionGroupMean[[1]])
                        }
                }
jtleek commented 10 years ago

Good idea. We would need to change downstream uses of foldChange with log2FoldChange. Could you issue a pull request with these changes made? That would be huge.

lcolladotor commented 10 years ago

Fixed in 78b70658b35fb30dc12b79237d68ef1710b5b712