StateQuantificationPlot: Plot states quantification bar

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

Plot states quantification bar

Description

Plot states quantification bar

Usage

StateQuantificationPlot(SortedReads)

Arguments

SortedReads

Sorted reads object as returned by SortReads function

Value

Bar plot quantifying states

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)
    StateQuantificationPlot(SortedReads = SortedReads)
}

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