setTrapParams: Set the parameters for running scAPAtrap

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

Set the parameters for running scAPAtrap

Description

setTrapParams sets parameters for running scAPAtrap, by setting default values using TRAP.PARAMS and checking the validity.

Usage

setTrapParams(trap.params = NULL, print = TRUE, check = TRUE, ...)

Arguments

trap.params	A list similar to TRAP.PARAMS.
print	Whether to print the list (default is TRUE).
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 like codeTRAP.PARAMS.

Examples

## get default
trap.params=setTrapParams()
## change some parameters
trap.params=setTrapParams(list(chrs=c('2L','2R','3L','3R','4','X','Y'), TenX=FALSE))
## will ignore non-valid parameter names
trap.params=setTrapParams(list(xx=FALSE))
## add barcodes
trap.params=setTrapParams(list(barcode=c('AAA','BBB')))
## not print
trap.params=setTrapParams(print=FALSE)

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