PlotSingleSiteSMF: Plot SMF data at single site

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

Plot SMF data at single site

Description

Plot SMF data at single site

Usage

PlotSingleSiteSMF(
  ContextMethylation,
  sample,
  range,
  SortedReads = NULL,
  TFBSs,
  saveAs = NULL
)

Arguments

ContextMethylation	Context methylation object as returned by CallContextMethylation function
sample	one sample as reported in the SampleName files of the QuasR sampleSheet
range	GRange 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
TFBSs	GRange or GRangesList of transcription factor binding sites to add to the plot. If SortedReads are passed, the format of TFBSs (GRanges vs GRangesList) will be used to determie if single molecules were sorted based on one or multiple TFs
saveAs	Full path to pdf file to save plot to. Defaults to NULL, in which case will only display

Value

Single site plot including average SMF signal, single molecules stack and state quantification 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)

    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)

    PlotSingleSiteSMF(ContextMethylation = Methylation,
                      sample = MySample,
                      range = Region_of_interest,
                      SortedReads = SortedReads,
                      TFBSs = TFBSs,
                      saveAs = NULL)
}

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