RMotifScan {esATAC} | R Documentation |
Search motif position in given genome regions according PWM matrix.
atacMotifScan(atacProc, peak = NULL, genome = NULL, motifPWM = NULL, min.score = "85%", scanO.dir = NULL, n.cores = NULL, prefix = NULL, use.SavedPWM = NULL, ...) ## S4 method for signature 'ATACProc' atacMotifScan(atacProc, peak = NULL, genome = NULL, motifPWM = NULL, min.score = "85%", scanO.dir = NULL, n.cores = NULL, prefix = NULL, use.SavedPWM = NULL, ...) motifscan(peak = NULL, genome = NULL, motifPWM = NULL, min.score = "85%", scanO.dir = NULL, n.cores = NULL, prefix = NULL, use.SavedPWM = NULL, ...)
atacProc |
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peak |
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genome |
A DNAString object. |
motifPWM |
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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. |
use.SavedPWM |
use local motif position information. This data is download or generate by users. it must be a rds file 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
atacPeakCalling
atacCutSiteCount
matchPWM
subsetByOverlaps
library(BSgenome.Hsapiens.UCSC.hg19) library(R.utils) p1bz <- system.file("extdata", "Example_peak1.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)) pwm <- readRDS(system.file("extdata", "motifPWM.rds", package="esATAC")) #motifscan(peak = peak1_path, genome = BSgenome.Hsapiens.UCSC.hg19, #motifPWM = pwm, prefix = "test")