SortReads: Sort reads by single TF

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

Sort reads by single TF

Description

Sort reads by single TF

Usage

SortReads(MethSM, TFBS, BinsCoord, SortByCluster)

Arguments

MethSM	Single molecule matrix
TFBS	Transcription factor binding site to use for sorting
BinsCoord	list of 3 bin coordinates relative to the center of the TFBS.
SortByCluster	T/F

Value

list of sorted reads

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)))
    BinsCoord = list(c(-35,-25), c(-15,15), c(25,35))

    SortedReads = SortReads(Methylation[[2]], TFBSs, BinsCoord, SortByCluster = FALSE)
}

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