setTools: Set tool names for running scAPAtrap

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

Set tool names for running scAPAtrap

Description

setTools sets tool names with full path for running scAPAtrap and checks the validity.

Usage

setTools(tools, check = TRUE, ...)

Arguments

tools	A list providing full path of four tools: samtools, umitools, featureCounts, star.
check	Whether to check the validity of values (default is TRUE).
...	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'.

Value

A list with tool names as the names of the list.

Examples

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')
## Not run: 
tools=setTools(tools)

## End(Not run)
tools=setTools(tools, check=FALSE)

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