PlotSM: Wrapper for PlotSingleMoleculeStack function

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

Wrapper for PlotSingleMoleculeStack function

Description

adds the convenience of arranging reads before plotting

Usage

PlotSM(MethSM, range, SortedReads = NULL)

Arguments

MethSM	Single molecule methylation matrix
range	GRanges interval to plot
SortedReads	Defaults to NULL, in which case will plot unsorted reads. Sorted reads object as returned by SortReads function or "HC" to perform hierarchical clustering

Value

Single molecule stack plot

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)

    PlotSM(MethSM = Methylation[[2]], range = Region_of_interest)
}

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