Mercurial > repos > iuc > deseq2
diff get_deseq_dataset.R @ 20:89d26b11d452 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
| author | iuc |
|---|---|
| date | Thu, 06 Dec 2018 15:49:22 -0500 |
| parents | c56e0689e46e |
| children | 0696db066a5b |
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--- a/get_deseq_dataset.R Tue Dec 04 08:19:06 2018 -0500 +++ b/get_deseq_dataset.R Thu Dec 06 15:49:22 2018 -0500 @@ -57,13 +57,16 @@ }) txdb <- makeTxDbFromGFF(gffFile) k <- keys(txdb, keytype = "TXNAME") - tx2gene <- select(txdb, k, "GENEID", "TXNAME") + tx2gene <- select(txdb, keys=k, columns="GENEID", keytype="TXNAME") + # Remove 'transcript:' from transcript IDs (when gffFile is a GFF3 from Ensembl and the transcript does not have a Name) + tx2gene$TXNAME <- sub('^transcript:', '', tx2gene$TXNAME) } try(txi <- tximport(txiFiles, type=txtype, tx2gene=tx2gene)) if (!exists("txi")) { - # Remove version from transcript IDs - tx2gene$TXNAME <- sub('\\.[0-9]+', '', tx2gene$TXNAME) - txi <- tximport(txiFiles, type=txtype, tx2gene=tx2gene) + # Remove version from transcript IDs in tx2gene... + tx2gene$TXNAME <- sub('\\.[0-9]+$', '', tx2gene$TXNAME) + # ...and in txiFiles + txi <- tximport(txiFiles, type=txtype, tx2gene=tx2gene, ignoreTxVersion=TRUE) } dds <- DESeqDataSetFromTximport(txi, subset(sampleTable, select=-c(filename)),