filterBisulfiteVariant


  a VRanges object output by NGS pipeline implemented in HTSeqGenie package


seqVariant


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


coverage


  the pre-calculated CpG-site information (by identifyCpG function)


CpGInfo


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


cleanVariant

minCoverage


  convert rate threshold used by filtering variants on non-CpG sites (cleanVariant is TRUE)


convertTh.nonCpG


a VRanges object output by NGS pipeline implemented in HTSeqGenie package


methods

The methyAnalysis package aims for the DNA methylation data
analysis and visualization. A MethyGenoSet class is defined to keep the
chromosome location information together with the data. The package also includes
functions of estimating the methylation levels from Methy-Seq data.

Pan Du

methyAnalysis

DNA methylation data analysis and visualization

filterBisulfiteVariant function

a VRanges object output by NGS pipeline implemented in HTSeqGenie package

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

the pre-calculated CpG-site information (by identifyCpG function)

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

convert rate threshold used by filtering variants on non-CpG sites (cleanVariant is TRUE)

filterBisulfiteVariant: filtering the variant calls of Bisulfite converted sequencing data

Description

Usage

Arguments

Value

Details

See Also