GetSingleMolMethMat: Get Single Molecule methylation matrix

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

Get Single Molecule methylation matrix

Description

Used internally as the first step in CallContextMethylation

Usage

GetSingleMolMethMat(QuasRprj, range, sample)

Arguments

QuasRprj	QuasR project object as returned by calling the QuasR function qAling on previously aligned data
range	GenimocRange representing the genomic region of interest
sample	One of the sample names as reported in the SampleName field of the QuasR pointer file provided to qAlign. N.b. all the files with the passed sample name will be used to call methylation

Value

Single molecule methylation matrix (all Cytosines)

Examples

Qinput = paste0(tempdir(), "/NRF1Pair_Qinput.txt")
library(BSgenome.Mmusculus.UCSC.mm10)

if(file.exists(Qinput)){
    QuasRprj = GetQuasRprj(Qinput, BSgenome.Mmusculus.UCSC.mm10)

    sample = readr::read_delim(Qinput, delim = "\t")$SampleName
    range = GRanges(seqnames = "chr6", ranges = IRanges(start = 88106000, end = 88106500), strand = "*")

    MethSM = GetSingleMolMethMat(QuasRprj, range, sample)
}

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