getMotifPWM {esATAC} | R Documentation

## Processing PFM or PWM file.

### Description

atacMotifScan and atacMotifScanPair accept PWM in a `list`, this function convert a PFM or PWM file(in JASPAR format) to a list in R.

### Usage

    getMotifPWM(motif.file = NULL, is.PWM = FALSE, JASPARdb = FALSE,
      Species = NULL, Name = NULL, ID = NULL)

### Arguments

`motif.file` | PFM or PWM file.
`is.PWM` | TRUE or FALSE. If TRUE, the input file contains PWM, do not need convert to PWM. If FALSE, the input file contains PFM, need convert to PWM. Default:FALSE.
`JASPARdb` | TRUE or FALSE. Whether use JASPAR database or not.
`Species` | Taxonomy ID. For human, it's 9606.
`Name` | The name of the transcription factor.
`ID` | The ID of the transcription factor.

### Details

Converting a PFM or PWM file(in JASPAR format) to a list in R.

### Value

A list contains PWM.

### Author(s)

Wei Zhang

### Examples

    # from files(user customized)
    pfm_file <- system.file("extdata", "CTCF.txt", package="esATAC")
    pwm_list <- getMotifPWM(motif.file = pfm_file, is.PWM = FALSE)

    # from JASPAR database
    pwm_list <- getMotifPWM(JASPARdb = TRUE, Name = "TFAP2A")

[Package esATAC version 1.0.23 Index]