countPeaks: Calculate the expression level of each peak in each cell with...

In BMILAB/scAPAtrap: Identification and Quantification of Alternative Polyadenylation Sites from Single-cell RNA-seq Data

Calculate the expression level of each peak in each cell with umi_tools

Description

Calculate the expression level of each peak in each cell with umi_tools

Usage

countPeaks(umitools.path, input, outputdir, TenX = TRUE, ...)

Arguments

umitools.path	The path of the umi_tools.
input	The final.bam file is generated by generateFinalBam.
outputdir	Output file directory.
TenX	Logical value, TRUE for 10X data or BAM resulted from STARsolo.
...	Arguments passed to other methods and/or advanced arguments. Advanced arguments: verbose If 'TRUE' basic status updates will be printed along the way. logf If not NULL, then it should be a character string denoting a file name. Then message will be written to 'logf'. notRun Default is FALSE. If 'TRUE', the Shell commands inside this function will not run but output the commad line.

Value

Full path of the <counts.tsv.gz> file in the outputdir directory

Examples

umitools.path <- '/home/aa/miniconda2/envs/umi_tools/bin/umi_tools'
input <- './data/final.bam'
outputdir <- './data'
## Not run: 
countPeaks(umitools.path, input, outputdir, TenX=TRUE)

## End(Not run)
countPeaks(umitools.path, input, outputdir, TenX=TRUE, notRun=TRUE)

BMILAB/scAPAtrap documentation built on Oct. 13, 2023, 2:36 a.m.