estimateMethySeq


  a VRanges object output by NGS pipeline implemented in HTSeqGenie package


seqVariant


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


coverage


  the precalculated CpG-site information (by identifyCpG function)


CpGInfo


  whether to merge the AT and GA conversion on opposite strands


mergeStrand


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


cleanVariant

minCoverage


Estimate the methylation level (Beta-value) of Methyl-Seq data, which is a VRanges object output by NGS pipeline 


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

estimateMethySeq function

a VRanges object output by NGS pipeline implemented in HTSeqGenie package

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

the precalculated CpG-site information (by identifyCpG function)

whether to merge the AT and GA conversion on opposite strands

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

Estimate the methylation level (Beta-value) of Methyl-Seq data, which is a VRanges object output by NGS pipeline

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

Description

Usage

Arguments

Value

Details

See Also

Examples