filterBisulfiteVariant {methyAnalysis} | R Documentation

## filtering the variant calls of Bisulfite converted sequencing data

### Description

a VRanges object output by NGS pipeline implemented in HTSeqGenie package

### Usage

    filterBisulfiteVariant(seqVariant, coverage, CpGInfo, cleanVariant = TRUE, minCoverage = 1, convertTh.nonCpG = 0.9)

### 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 pre-calculated CpG-site information (by identifyCpG function)
`cleanVariant` | whether to filter those variants on non-CpG sites with full CT and GA conversion, or non CT and GA variations
`minCoverage` | minimum coverage for the variants
`convertTh.nonCpG` | convert rate threshold used by filtering variants on non-CpG sites (cleanVariant is TRUE)

### Details

Filtering the variant calls based on following criteria: Only keeps CG and GA conversion variants. The variants should have minimum coverage. When cleanVariant parameter is TRUE, those fully converted non-CpG sites (convert rate higher than convertTh.nonCpG) will be removed.

### Value

a filtered VRanges object with two attributes: 'variantStats' and 'filterSettings'

### Author(s)

Pan Du

### See Also

`estimateMethySeq`

[Package methyAnalysis version 1.28.0 Index]