methylglm {methylGSA} | R Documentation |
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" or "promoter". Default is "all". |
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 |
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)