comparison get_deseq_dataset.R @ 20:89d26b11d452 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459

19:c56e0689e46e

        suppressPackageStartupMessages({
          library("GenomicFeatures")
        })
        txdb <- makeTxDbFromGFF(gffFile)
        k <- keys(txdb, keytype = "TXNAME")
        tx2gene <- select(txdb, k, "GENEID", "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)
      }
      dds <- DESeqDataSetFromTximport(txi,
                                      subset(sampleTable, select=-c(filename)),
                                      designFormula)
  }

20:89d26b11d452

        suppressPackageStartupMessages({
          library("GenomicFeatures")
        })
        txdb <- makeTxDbFromGFF(gffFile)
        k <- keys(txdb, keytype = "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 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)),
                                      designFormula)
  }