Mercurial > repos > mingchen0919 > aurora_deseq2

diff rmarkdown_report.Rmd @ 18:81dd7b8c8118 draft

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planemo upload commit c3ae92f8087d0c69a7b9dd447d6060090a784bb1-dirty
author mingchen0919
date Thu, 13 Sep 2018 11:01:36 -0400
parents e71513809449
children 24a7f1f92db7
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--- a/rmarkdown_report.Rmd	Sat Jun 09 22:58:53 2018 -0400
+++ b/rmarkdown_report.Rmd	Thu Sep 13 11:01:36 2018 -0400
@@ -66,6 +66,11 @@
 dds = DESeqDataSetFromMatrix(countData = count_data,
                              colData = coldata,
                              design = formula(opt$X_C))
+
+# prefiltering
+keep <- rowSums(counts(dds)) >= 10
+dds <- dds[keep,]
+
 dds = DESeq(dds, test = opt$X_G, fitType = opt$X_H)
 ## Differential expression test results
 res = results(dds, contrast = c(opt$X_D, opt$X_E, opt$X_F), alpha = opt$X_I)