filterBisulfiteVariant: filtering the variant calls of Bisulfite converted sequencing...
In methyAnalysis: DNA methylation data analysis and visualization

Description Usage Arguments Details Value Author(s) See Also

a VRanges object output by NGS pipeline implemented in HTSeqGenie package

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

`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)

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.

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

Pan Du

estimateMethySeq

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