Description Usage Arguments Value See Also
Extracts raw counts from each of the "abundance.tsv" files generated by kallisto (https://pachterlab.github.io/kallisto/about) expression analysis. The counts are put into a matrix (genes by sample), and rounded. This step collects the raw count data ready for further expression analysis, or for differential expression, using DESeq2
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1 | collectKallistoCounts(baseDir = "./kallistoResults")
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baseDir |
A character string of the directory where kallisto results are stored. For example, baseDir = "kallistoResults" will search "kallistoResults/*/abundance.tsv". |
matrix. A matrix of (rounded) raw counts of genes (or transcripts) for each sample.
kallisto (https://pachterlab.github.io/kallisto/about)
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