initScAPAtrap: Initiate scAPAtrap and check/set parameters

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

Initiate scAPAtrap and check/set parameters

Description

Initiate scAPAtrap and check/set parameters

Usage

initScAPAtrap(tools, trap.params, inputBam, outputDir, ...)

Arguments

tools	A list contains four tools used in scAPAtrap.
trap.params	Parameters of running scAPAtrap, see global variable TRAP.PARAMS.
inputBam	Input bam file name. If trap.params$chr is NULL, will try to get chrs from inputBam.
outputDir	Output dir for storing scAPAtrap's final output – peaks and counts files. If only dirname is given (e.g., APAres but not ./APAres), then will add path of inputBam to the dir name. If outputDir already exists, an error will be raised to avoid overwritting. However, many temporary files are generated during running scAPAtrap, which could be seen from global variable TRAPFILES. Those files marked with * could be savely deleted.
...	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. If logf is a character string, then message will be written to 'logf'. But if logf already exists, this function will quit to avoid overwriting an existing log file. The logf will log full information during scAPAtrap, including time, command, and output files.

Value

NULL. But the input tools, trap.params, inputBam, outputDir may be modifed during initiation.

Examples

## Not run: 
tools=list(samtools='/home/dell/miniconda3/envs/scAPA/bin/samtools',
           umitools='/home/dell/miniconda3/envs/scAPA/bin/umi_tools',
           featureCounts="/home/dell/miniconda3/envs/scAPA/bin/featureCounts",
           star='/home/dell/miniconda3/envs/scAPA/bin/STAR')
trap.params=TRAP.PARAMS()
trap.params$chr=1:3

## input BAM
dir0='/mnt/64cf3476-350c-46ad-bc48-574fa64a0334/test/xwu/dataFly/'
inputBam=paste0(dir0, "filterCB.bam")

## log file
logf=gsub('.bam', '.scAPAtrap.log', inputBam, fixed=TRUE)

## output dir (will be under inputBam's dir)
outputDir="APA.result"

## one step scAPAtrap
initScAPAtrap(tools=tools, trap.params=trap.params,
         inputBam=inputBam, outputDir=outputDir, logf=logf)

## End(Not run)
## just test the function with toCheck=FALSE
initScAPAtrap(tools='just-for-fun.tools',
              trap.params=list('just-for-fun.params'),
              inputBam='just-for-fun.bam', outputDir='just-for-fun.dir', toCheck=FALSE)
trap.params

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