estimateMethySeq {methyAnalysis} | R Documentation |
Estimate the methylation level (Beta-value) of Methyl-Seq data, which is a VRanges object output by NGS pipeline
estimateMethySeq(seqVariant, coverage, CpGInfo = NULL, mergeStrand = TRUE, cleanVariant = TRUE, minCoverage = 10)
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 |
a GRanges object with the Beta column shows the methylation levels
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