prepareAnnot: Prepare user-supplied mapping between CpGs and genes.

In methylGSA: Gene Set Analysis Using the Outcome of Differential Methylation

Description

This function prepares CpG to gene mapping which will be used by methylRRA and methylglm.

Usage

prepareAnnot(CpG2Gene, geneidtype = "SYMBOL")

Arguments

CpG2Gene	A matrix, or a data frame or a list contains CpG to gene mapping. For a matrix or data frame, 1st column should be CpG ID and 2nd column should be gene name. For a list, entry names should be gene names, and elements correpond to CpG IDs.
geneidtype	A string. "SYMBOL", "ENSEMBL", "ENTREZID" or "REFSEQ". Default is "SYMBOL".

Value

A data frame contains ready to use CpG to gene mapping.

References

Carlson M (2017). org.Hs.eg.db: Genome wide annotation for Human. R package version 3.5.0.

Examples

data(CpG2Genetoy)
FullAnnot = prepareAnnot(CpG2Gene)
head(FullAnnot)

methylGSA documentation built on Nov. 8, 2020, 8:29 p.m.