CallContextMethylation: Call Context Methylation

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

Call Context Methylation

Description

Can deal with multiple samples

Usage

CallContextMethylation(
  sampleSheet,
  sample,
  genome,
  range,
  coverage = 20,
  ConvRate.thr = 0.2
)

Arguments

sampleSheet	QuasR pointer file
sample	for now this works for sure on one sample at the time only
genome	BSgenome
range	GenimocRange representing the genomic region of interest
coverage	coverage threshold. Defaults to 20.
ConvRate.thr	Convesion rate threshold. Double between 0 and 1, defaults to 0.2

Value

List with two Granges objects: average methylation call (GRanges) and single molecule methylation call (matrix)

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)
}

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