FilterContextCytosines: Filter Cytosines in context

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

Filter Cytosines in context

Description

Filter Cytosines in context

Usage

FilterContextCytosines(MethGR, genome, context)

Arguments

MethGR	Granges obj of average methylation
genome	BSgenome
context	Context of interest (e.g. "GC", "CG",..)

Value

filtered Granges obj

Examples

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

if(file.exists(Qinput)){
    QuasRprj = GetQuasRprj(Qinput, BSgenome.Mmusculus.UCSC.mm10)

    Samples = readr::read_delim(Qinput, delim = "\t")$SampleName
    sample = Samples[1]
    range = GRanges(seqnames = "chr6", ranges = IRanges(start = 88106000, end = 88106500), strand = "*")

    MethGR = QuasR::qMeth(QuasRprj[grep(sample, Samples)], mode="allC", range, collapseBySample = TRUE, keepZero = TRUE)
    FilterContextCytosines(MethGR, BSgenome.Mmusculus.UCSC.mm10, "NGCNN")
}

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