collectKallistoCountsTXItoGene: Collects raw counts of genes, based on transcript data...
In nixstix/RNASeqAnalysis: Analysis of RNA-Seq data: QC filtering, expression analysis, differential expression pipeline
Description
Usage
Arguments
Value
Description
Extracts raw counts of transcripts from each of the "abundance.tsv" files generated by kallisto (https://pachterlab.github.io/kallisto/about) expression analysis and converts this to gene counts. The counts are put into a matrix (genes by sample). This step collects the raw count data ready for further expression analysis, or for differential expression, using DESeq2.
Usage
1
collectKallistoCountsTXItoGene(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 raw counts of genes for each sample.
nixstix/RNASeqAnalysis documentation built on May 23, 2019, 7:06 p.m.
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Description Usage Arguments Value
Description
Extracts raw counts of transcripts from each of the "abundance.tsv" files generated by kallisto (https://pachterlab.github.io/kallisto/about) expression analysis and converts this to gene counts. The counts are put into a matrix (genes by sample). This step collects the raw count data ready for further expression analysis, or for differential expression, using DESeq2.
Usage
1 | collectKallistoCountsTXItoGene(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 raw counts of genes for each sample.
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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