methylgometh {methylGSA} | R Documentation |
This function calls gometh or gsameth function in missMethyl package to adjust number of probes in gene set testing
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)
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. |
A data frame contains gene set tests results.
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.
## 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)