scanGenomeMotif {esATAC}R Documentation

Scan motif position.

Description

Scan motif position from the given genome.

Usage

scanGenomeMotif(motifPWM = NULL, refgenome = NULL, min.score = NULL,
  n.core = NULL, output = NULL)

Arguments

motifPWM

list scalar. Every element in the list contains a motif PWM matrix.

refgenome

reference genome.

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.

n.core

How many core to run this function.

output

Where to save the result, please with suffix ".rds".

Details

Scan motif position from the given genome.

Value

the result of saveRDS

Author(s)

Wei Zhang

Examples


pwm <- readRDS(system.file("extdata", "motifPWM.rds", package="esATAC"))
#library(BSgenome.Hsapiens.UCSC.hg19)
#scanGenomeMotif(motifPWM = pwm, refgenome = BSgenome.Hsapiens.UCSC.hg19,
#min.score = "90%", n.core = 2, output = "motif.rds")


[Package esATAC version 1.0.23 Index]