methylglm: Implement logistic regression adjusting for number of probes...
In methylGSA: Gene Set Analysis Using the Outcome of Differential Methylation

Description Usage Arguments Details Value References Examples

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

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())

`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.

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

A data frame contains gene set tests results.

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.

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)