methylglm {methylGSA} | R Documentation

## Implement logistic regression adjusting for number of probes in enrichment analysis

### Description

This function implements logistic regression adjusting for number of probes in enrichment analysis.

### Usage

    methylglm(cpg.pval, array.type = "450K", FullAnnot = NULL,
      group = "all", GS.list = NULL, GS.idtype = "SYMBOL",
      GS.type = "GO", minsize = 100, maxsize = 500, parallel = FALSE,
      BPPARAM = bpparam())

### Arguments

`cpg.pval` | A named vector containing p-values of differential methylation test. Names should be CpG IDs.
`array.type` | A string. Either "450K" or "EPIC". Default is "450K". This argument will be ignored if FullAnnot is provided.
`FullAnnot` | A data frame provided by prepareAnnot function. Default is NULL.
`group` | A string. "all", "body", "promoter1" or "promoter2". Default is "all". If group = "body", only CpGs on gene body will be considered in methylglm. If group = "promoter1" or group = "promoter2", only CpGs on promoters will be considered. Here is the definition of "body", "promoter1" and "promoter2" according to the annotation in IlluminaHumanMethylation450kanno.ilmn12.hg19 or IlluminaHumanMethylationEPICanno.ilm10b4.hg19. body: CpGs whose gene group correspond to "Body" or "1stExon" promoter1: CpGs whose gene group correspond to "TSS1500" or "TSS200" promoter2: CpGs whose gene group correspond to "TSS1500", "TSS200", "1stExon", or "5'UTR". If group = "all", all CpGs are considered regardless of their gene group.
`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". Default is "GO"
`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.
`parallel` | either TRUE or FALSE indicating whether parallel should be used. Default is FALSE
`BPPARAM` | an argument provided to `bplapply`. See `register` for details.

### Details

The implementation of this function is modified from goglm function in GOglm package.

### Value

A data frame contains gene set tests results.

### References

Mi G, Di Y, Emerson S, Cumbie JS and Chang JH (2012) Length bias correction in Gene Ontology enrichment analysis using logistic regression. PLOS ONE, 7(10): e46128

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

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

### Examples

    data(CpG2Genetoy)
    data(cpgtoy)
    data(GSlisttoy)
    GS.list = GS.list[1:10]
    FullAnnot = prepareAnnot(CpG2Gene)
    res = methylglm(cpg.pval = cpg.pval, FullAnnot = FullAnnot,
    GS.list = GS.list, GS.idtype = "SYMBOL")
    head(res)

[Package methylGSA version 1.10.0 Index]