estimateMethySeq {methyAnalysis}R Documentation

Estimate the methylation level (Beta-value) of Methyl-Seq data

Description

Estimate the methylation level (Beta-value) of Methyl-Seq data, which is a VRanges object output by NGS pipeline

Usage

estimateMethySeq(seqVariant, coverage, CpGInfo = NULL, mergeStrand = TRUE, cleanVariant = TRUE, minCoverage = 10)

Arguments

seqVariant

a VRanges object output by NGS pipeline implemented in HTSeqGenie package

coverage

the genome coverage (a RleList object) output by NGS pipeline

CpGInfo

the precalculated CpG-site information (by identifyCpG function)

mergeStrand

whether to merge the AT and GA conversion on opposite strands

cleanVariant

whether to filter those non-CpG with full CT and GA conversion, or non CT and GA variations

minCoverage

minimum coverage for the variants

Value

a GRanges object with the Beta column shows the methylation levels

Author(s)

Pan Du


[Package methyAnalysis version 1.30.0 Index]