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 1.22.0 Index]