Tximport > DESeq2 (sample names)
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2.9 years ago
Barry Digby ▴ 780

Using R and tximport, I have read in 6 t_data.ctab files to create a DESeqDataSet by using DESeqDataSetFromTximport.

When plotting heatmaps etc, the sample names are '1', '2', '3', '4', '5', '6'. I suspect it has something to do with reading in the ctab files, when i run txi$counts the column headers are:

     [,1]  [,2]  [,3]  [,4]  [,5]  [,6]
  

I'm basing this on the bioconductor vignette: "The user should make sure the rownames of sampleTable align with the colnames of txi$counts, if there are colnames."

data <- c("/Users/Desktop/read_tables/H84S2Ctrl_S7/t_data.ctab",
      "/Users/Desktop/read_tables/H84WTCtrl_S1/t_data.ctab",
      "/Users/Desktop/read_tables/H85S2Ctrl_S8/t_data.ctab",
      "/Users/Desktop/read_tables/H85WTCtrl_S2/t_data.ctab",
      "/Users/Desktop/read_tables/H86S2Ctrl_S9/t_data.ctab",
      "/Users/Desktop/read_tables/H86WTCtrl_S3/t_data.ctab")

tmp <- read.table(data[1], header = TRUE)

tx2gene <- tmp[, c("t_name", "gene_name")]

txi <- tximport(data, type = "stringtie", tx2gene = tx2gene)

sampleNames <- c("S2Ctrl_7", "WTCtrl_1", "S2Ctrl_8", "WTCtrl_2", "S2Ctrl_9", "WTCtrl_3")

sampleGroup <- c("S2", "WT", "S2", "WT", "S2", "WT")

sampleTable <- data.frame(sampleName = sampleNames, type = sampleGroup)

rownames(sampleTable) <- colnames(txi$counts)

ddsTxi <- DESeqDataSetFromTximport(txi, sampleTable, design = ~ type)

dds <- DESeq(ddsTxi)

How can I assign the correct sample names and not 1, 2, 3, 4....?

Thank you in advance for your time

DESeq2 tximport RNA-Seq • 3.4k views
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heatmap image:

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3
Entering edit mode
2.9 years ago
Barry Digby ▴ 780

Adding:

names(data) <- c("S2Ctrl_7", "WTCtrl_1", "S2Ctrl_8", "WTCtrl_2", "S2Ctrl_9", "WTCtrl_3")

below 'data' did the trick for anyone who has the same problem down the line..

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