tsvToMethMat: Convert nanopore tsv to methylation matrix

In jsemple19/nanodsmf: Analyse nanopore dual enzyme single molecule footprinting data (nanoDSMF)

Description

Convert nanopore tsv to methylation matrix

Usage

tsvToMethMat(tsv, genomeGRs, motif, binarise = TRUE)

Arguments

tsv	A tab serparated values text file where individual motifs have been split. Also accepts a Granges object made from tsv
genomeGRs	Genomic Ranges object for the regions to be analysed
motif	Motif ("CG" or "GC" to for which the tsv was called)
binarise	Convert log likelihoods to binary values: methylated(ln(L) ≥ 2.5): 1; unmethylated(ln(L) ≤ -2.5): 0; inconclusive(-2.5 < ln(L) < 2.5): NA. (default: binarise=TRUE)

Value

A methylation matrix (reads x motif positions) with binary or log likelihood values

Examples

tsvToMethMat(splitMotifs(MSssI_CpG,"CG"),ttTi5605gr)

jsemple19/nanodsmf documentation built on July 23, 2020, 7:40 a.m.