SortReadsByTFCluster: Wrapper to SortReads for TF cluster case

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

Wrapper to SortReads for TF cluster case

Description

Wrapper to SortReads for TF cluster case

Usage

SortReadsByTFCluster(MethSM, TFBSs)

Arguments

MethSM	Single molecule matrix
TFBSs	Transcription factor binding sites to use for sorting, passed as a GRanges object of length > 1

Value

List of reads sorted by TF cluster

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)))

    SortedReads = SortReadsByTFCluster(MethSM = Methylation[[2]], TFBSs = TFBSs)
}

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