estimateMethySeq: Estimate the methylation level (Beta-value) of Methyl-Seq...

In methyAnalysis: DNA methylation data analysis and visualization

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

methyAnalysis documentation built on Nov. 8, 2020, 8:09 p.m.