CallContextMethylation {SingleMoleculeFootprinting}R Documentation

Call Context Methylation

Description

Can deal with multiple samples

Usage

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

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

verbose

TRUE/FALSE

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)
}


[Package SingleMoleculeFootprinting version 1.0.0 Index]