mkatari-bioinformatics-august-2013-deseq
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Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
mkatari-bioinformatics-august-2013-deseq [2015/06/17 06:15] – mkatari | mkatari-bioinformatics-august-2013-deseq [2015/06/17 08:19] – mkatari | ||
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First we will load the count data file. | First we will load the count data file. | ||
< | < | ||
- | counts = read.table(pathToCountsData, header=T, row.names=1) | + | counts = read.table(" |
</ | </ | ||
Line 58: | Line 58: | ||
To visualize the disperson graph | To visualize the disperson graph | ||
< | < | ||
- | dispersionFile = paste(pathToOutputDir, | + | dispersionFile = " |
pdf(dispersionFile) | pdf(dispersionFile) | ||
plotDispEsts( cds ) | plotDispEsts( cds ) | ||
Line 77: | Line 77: | ||
< | < | ||
- | maFile = paste(pathToOutputDir, | + | maFile = " |
pdf(maFile) | pdf(maFile) | ||
plotMA(res) | plotMA(res) | ||
Line 87: | Line 87: | ||
resSig = res[ which(res$padj < 0.1), ] | resSig = res[ which(res$padj < 0.1), ] | ||
- | outfile = paste(pathToOutputDir, | + | outfile = " |
write.table(resSig, | write.table(resSig, |
mkatari-bioinformatics-august-2013-deseq.txt · Last modified: 2015/08/21 14:13 by mkatari