methylgometh {methylGSA} | R Documentation

## Adjusting number of probes in gene set testing using gometh or gsameth in missMethyl

### 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)

[Package methylGSA version 1.0.4 Index]