methylgometh: Adjusting number of probes in gene set testing using gometh...

In reese3928/methylGSA: Gene Set Analysis Using the Outcome of Differential Methylation

Description

This function calls gometh or gsameth function in missMethyl package to adjust number of probes in gene set testing

Usage

methylgometh(cpg.pval, sig.cut = 0.001, topDE = NULL,
  array.type = "450K", GS.list = NULL, GS.idtype = "SYMBOL",
  GS.type = "GO", minsize = 100, maxsize = 500)

Arguments

cpg.pval	A named vector containing p-values of differential methylation test. Names should be CpG IDs.
sig.cut	A numeric value indicating cut-off value for significant CpG. Default is 0.001. This argument will be ignored if topDE is provided.
topDE	An integer. The top number of CpGs to be declared as significant.
array.type	A string. Either "450K" or "EPIC". Default is "450K".
GS.list	A list. Default is NULL. If there is no input list, Gene Ontology is used. Entry names are gene sets names, and elements correpond to genes that gene sets contain.
GS.idtype	A string. "SYMBOL", "ENSEMBL", "ENTREZID" or "REFSEQ". Default is "SYMBOL".
GS.type	A string. "GO", "KEGG", or "Reactome"
minsize	An integer. If the number of genes in a gene set is less than this integer, this gene set is not tested. Default is 100.
maxsize	An integer. If the number of genes in a gene set is greater than this integer, this gene set is not tested. Default is 500.

Value

A data frame contains gene set tests results.

References

Phipson, B., Maksimovic, J., and Oshlack, A. (2015). missMethyl: an R package for analysing methylation data from Illuminas HumanMethylation450 platform. Bioinformatics, btv560.

Ligtenberg W (2017). reactome.db: A set of annotation maps for reactome. R package version 1.62.0.

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

Examples

## Not run: 
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
data(cpgtoy)
res = methylgometh(cpg.pval = cpg.pval, sig.cut = 0.001, GS.type = "KEGG",
minsize = 200, maxsize = 205)
head(res)

## End(Not run)

reese3928/methylGSA documentation built on May 10, 2021, 10:41 p.m.