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]