Mercurial > repos > iuc > deseq2

comparison deseq2.R @ 11:25204a860b79 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
author iuc
date Sun, 28 Jan 2018 04:04:12 -0500
parents 6f91b8ce6e07
children bd06df00180a
comparison
equal deleted inserted replaced
10:24a09ca67621 11:25204a860b79
53 "countsfile", "n", 1, "character", 53 "countsfile", "n", 1, "character",
54 "factors", "f", 1, "character", 54 "factors", "f", 1, "character",
55 "plots" , "p", 1, "character", 55 "plots" , "p", 1, "character",
56 "sample_table", "s", 1, "character", 56 "sample_table", "s", 1, "character",
57 "tximport", "i", 0, "logical", 57 "tximport", "i", 0, "logical",
58 "txtype", "y", 1, "character",
58 "tx2gene", "x", 1, "character", # a space-sep tx-to-gene map or GTF file (auto detect .gtf/.GTF) 59 "tx2gene", "x", 1, "character", # a space-sep tx-to-gene map or GTF file (auto detect .gtf/.GTF)
59 "fit_type", "t", 1, "integer", 60 "fit_type", "t", 1, "integer",
60 "many_contrasts", "m", 0, "logical", 61 "many_contrasts", "m", 0, "logical",
61 "outlier_replace_off" , "a", 0, "logical", 62 "outlier_replace_off" , "a", 0, "logical",
62 "outlier_filter_off" , "b", 0, "logical", 63 "outlier_filter_off" , "b", 0, "logical",
236 tx2gene <- df[, 2:1] # tx ID, then gene ID 237 tx2gene <- df[, 2:1] # tx ID, then gene ID
237 } 238 }
238 library("tximport") 239 library("tximport")
239 txiFiles <- as.character(sampleTable[,2]) 240 txiFiles <- as.character(sampleTable[,2])
240 names(txiFiles) <- as.character(sampleTable[,1]) 241 names(txiFiles) <- as.character(sampleTable[,1])
241 txi <- tximport(txiFiles, type="sailfish", tx2gene=tx2gene) 242 txi <- tximport(txiFiles, type=opt$txtype, tx2gene=tx2gene)
242 dds <- DESeqDataSetFromTximport(txi, 243 dds <- DESeqDataSetFromTximport(txi,
243 sampleTable[,3:ncol(sampleTable),drop=FALSE], 244 sampleTable[,3:ncol(sampleTable),drop=FALSE],
244 designFormula) 245 designFormula)
245 } 246 }
246 247