RMotifScanPair {esATAC} | R Documentation |
Search motif position in given genome regions according PWM matrix.
atacMotifScanPair(atacProc, peak1 = NULL, peak2 = NULL, background = NULL, genome = NULL, motifPWM = NULL, min.score = "85%", scanO.dir = NULL, n.cores = NULL, prefix = NULL, use.SavedPWM = NULL, ...) ## S4 method for signature 'ATACProc' atacMotifScanPair(atacProc, peak1 = NULL, peak2 = NULL, background = NULL, genome = NULL, motifPWM = NULL, min.score = "85%", scanO.dir = NULL, n.cores = NULL, prefix = NULL, use.SavedPWM = NULL, ...) motifscanpair(peak1 = NULL, peak2 = NULL, background = NULL, genome = NULL, motifPWM = NULL, min.score = "85%", scanO.dir = NULL, n.cores = NULL, prefix = NULL, use.SavedPWM = NULL, ...)
atacProc |
|
peak1 |
peak file path. |
peak2 |
peak file path. |
background |
background peak file path. |
genome |
A DNAString object. |
motifPWM |
|
min.score |
The minimum score for counting a match. Can be given as a character string containing a percentage (e.g. "85 possible score or as a single number. |
scanO.dir |
|
n.cores |
How many core to run this function.
Default: from |
prefix |
prefix for Output file. Order: peak1, peak2, backgroud. |
use.SavedPWM |
use local motif position information. This data is download or generate by users. It must be a rds file (generated by R) and the information saved as GRanges. Once this parameter is used, parameters "genome", "motifPWM", "min.score", "n.cores" will be set to NULL. |
... |
Additional arguments, currently unused. |
This function scan motif position in a given genome regions.
An invisible ATACProc-class
object scalar for
downstream analysis.
Wei Zhang
library(R.utils) library(BSgenome.Hsapiens.UCSC.hg19) p1bz <- system.file("extdata", "Example_peak1.bed.bz2", package="esATAC") p2bz <- system.file("extdata", "Example_peak2.bed.bz2", package="esATAC") peak1_path <- as.vector(bunzip2(filename = p1bz, destname = file.path(getwd(), "Example_peak1.bed"), ext="bz2", FUN=bzfile, overwrite=TRUE , remove = FALSE)) peak2_path <- as.vector(bunzip2(filename = p2bz, destname = file.path(getwd(), "Example_peak2.bed"), ext="bz2", FUN=bzfile, overwrite=TRUE, remove = FALSE)) peakcom.output <- peakcomp(bedInput1 = peak1_path, bedInput2 = peak2_path, olap.rate = 0.1) pwm <- readRDS(system.file("extdata", "motifPWM.rds", package="esATAC")) ## Not run: output <- atacMotifScanPair(atacProc = peakcom.output, genome = BSgenome.Hsapiens.UCSC.hg19, motifPWM = pwm) ## End(Not run)