collectKallistoCounts: Collects raw counts of gene (or transcript) data generated by...
In nixstix/RNASeqAnalysis: Analysis of RNA-Seq data: QC filtering, expression analysis, differential expression pipeline
Description
Usage
Arguments
Value
See Also
Description
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.
Usage
1
collectKallistoCounts(baseDir = "./kallistoResults")
Arguments
baseDir
A character string of the directory where kallisto results are stored. For example, baseDir = "kallistoResults" will search "kallistoResults/*/abundance.tsv".
Value
matrix. A matrix of (rounded) raw counts of genes (or transcripts) for each sample.
See Also
kallisto (https://pachterlab.github.io/kallisto/about)
nixstix/RNASeqAnalysis documentation built on May 23, 2019, 7:06 p.m.
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Description Usage Arguments Value See Also
Description
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.
Usage
1 | collectKallistoCounts(baseDir = "./kallistoResults")
|
Arguments
baseDir |
A character string of the directory where kallisto results are stored. For example, baseDir = "kallistoResults" will search "kallistoResults/*/abundance.tsv". |
Value
matrix. A matrix of (rounded) raw counts of genes (or transcripts) for each sample.
See Also
kallisto (https://pachterlab.github.io/kallisto/about)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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