Mercurial > repos > iuc > deseq2

comparison get_deseq_dataset.R @ 30:8fe98f7094de draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
author iuc
date Fri, 26 Aug 2022 11:16:15 +0000
parents de44f8eff84a
children
comparison
equal deleted inserted replaced
29:cd9874cb9019 30:8fe98f7094de
12 gff_file <- NULL 12 gff_file <- NULL
13 tx2gene <- read.table(tx2gene, header = has_header) 13 tx2gene <- read.table(tx2gene, header = has_header)
14 } 14 }
15 } 15 }
16 16
17 if (!use_txi & has_header) { 17 if (!use_txi && has_header) {
18 countfiles <- lapply(as.character(sample_table$filename), read.delim, row.names = 1) 18 countfiles <- lapply(as.character(sample_table$filename), read.delim, row.names = 1)
19 tbl <- do.call("cbind", countfiles) 19 tbl <- do.call("cbind", countfiles)
20 colnames(tbl) <- rownames(sample_table) # take sample ids from header 20 colnames(tbl) <- rownames(sample_table) # take sample ids from header
21 21
22 # check for htseq report lines (from DESeqDataSetFromHTSeqCount function) 22 # check for htseq report lines (from DESeqDataSetFromHTSeqCount function)
33 dds <- DESeqDataSetFromMatrix( 33 dds <- DESeqDataSetFromMatrix(
34 countData = tbl, 34 countData = tbl,
35 colData = subset(sample_table, select = -filename), 35 colData = subset(sample_table, select = -filename),
36 design = design_formula 36 design = design_formula
37 ) 37 )
38 } else if (!use_txi & !has_header) { 38 } else if (!use_txi && !has_header) {
39 39
40 # construct the object from HTSeq files 40 # construct the object from HTSeq files
41 dds <- DESeqDataSetFromHTSeqCount( 41 dds <- DESeqDataSetFromHTSeqCount(
42 sampleTable = sample_table, 42 sampleTable = sample_table,
43 directory = dir, 43 directory = dir,