merge_cpg_dinucleotide_methylation: Merge methylation for CpG dinucleotide

In jokergoo/epik: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Merge methylation for CpG dinucleotide

Usage

merge_cpg_dinucleotide_methylation(pos, meth, cov)

Arguments

pos	positions of CpG sites, must be sorted
meth	methylation matrix associated with the CpG positions. Note the value should be the number of methylated CpGs at each CpG site
cov	CpG coverage matrix

Details

Normally methylation for the two Cs in a CpG dinucleotide (a second C is on the other strand) is very similar. This function helps to reduce the redundency of the methylation dataset.

For two Cs in a CpG dinucleotide, the merged methylation value (the methylated Cs) is calculated by weighting the CpG coverage of the two Cs. Also the merged coverage is also calculated by weighting the coverage itself.

Value

a list containg a pos vector, a meth matrix and a cov matrix

Author(s)

Zuguang Gu <[e-mail]>

Examples

# There is no example
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jokergoo/epik documentation built on Sept. 28, 2019, 9:20 a.m.