BinMethylation: Summarize methylation inside sorting bins

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

Summarize methylation inside sorting bins

Description

Summarize methylation inside sorting bins

Usage

BinMethylation(MethSM, TFBS, bin)

Arguments

MethSM	Single molecule matrix
TFBS	Transcription factor binding site to use for sorting, passed as a GRanges object of length 1
bin	vector of two integers representing the coordinate of a bin relative to the center of the TFBS

Value

Reads covering bin with their summarized methylation status

Examples

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

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

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

    Methylation = CallContextMethylation(sampleSheet = Qinput,
                                     sample = MySample,
                                     genome = BSgenome.Mmusculus.UCSC.mm10,
                                     range = Region_of_interest,
                                     coverage = 20,
                                     ConvRate.thr = 0.2)

    TFBSs = GenomicRanges::GRanges("chr6", IRanges(c(88106253), c(88106263)), strand = "-")
    elementMetadata(TFBSs)$name = c("NRF1")
    names(TFBSs) = c(paste0("TFBS_", c(4305216)))

    binMethylationValues = BinMethylation(MethSM = Methylation[[2]], TFBS = TFBSs, bin = c(-15,15))
}

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