PlotAvgSMF: Plot average methylation

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

Plot average methylation

Description

Plot average methylation

Usage

PlotAvgSMF(MethGR, range, TFBSs)

Arguments

MethGR	Average methylation GRanges obj
range	GRanges interval to plot
TFBSs	GRanges object of transcription factor binding sites to include in the plot. Assumed to be already subset.

Value

Average SMF signal at single site

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)))

    PlotAvgSMF(MethGR = Methylation[[1]], range = Region_of_interest, TFBSs = TFBSs)
}

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