getMotifPWM {esATAC} | R Documentation |
atacMotifScan and atacMotifScanPair accept PWM in a list
, this
function convert a PFM or PWM file(in JASPAR format) to a list in R.
getMotifPWM(motif.file = NULL, is.PWM = FALSE, JASPARdb = FALSE, Species = NULL, Name = NULL, ID = NULL)
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. |
Converting a PFM or PWM file(in JASPAR format) to a list in R.
A list contains PWM.
Wei Zhang
# 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")