BaitCapture: Bait capture efficiency

In Krebslabrep/SingleMoleculeFootprinting: Analysis tools for Single Molecule Footprinting (SMF) data

Bait capture efficiency

Description

check bait capture efficiency. Expected to be ~70

Usage

BaitCapture(sampleSheet, genome, baits, cores = 1)

Arguments

sampleSheet	QuasR sample sheet
genome	BS genome
baits	Full path to bed file containing bait coordinates. If chromosome names are in e.g. "1" format, they'll be temporarily converted to "chr1"
cores	number of cores for parallel processing. Defaults to 1

Value

bait capture efficiency

Examples

Qinput = paste0(tempdir(), "/NRF1Pair_Qinput.txt")
library(BSgenome.Mmusculus.UCSC.mm10)

if(file.exists(Qinput)){
    # DO NOT RUN
    # BaitRegions = SingleMoleculeFootprintingData::EnrichmentRegions_mm10.rds()
    # BaitCaptureEfficiency = BaitCapture(sampleSheet = Qinput, genome = BSgenome.Mmusculus.UCSC.mm10, baits = BaitRegions)
}

Krebslabrep/SingleMoleculeFootprinting documentation built on Nov. 19, 2022, 3:56 a.m.