## ---- echo = FALSE------------------------------------------------------------ knitr::opts_chunk$set(comment = "", message=FALSE, warning = FALSE) ## ----eval = FALSE------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("methylGSA") ## ----------------------------------------------------------------------------- library(methylGSA) ## ----------------------------------------------------------------------------- library(IlluminaHumanMethylation450kanno.ilmn12.hg19) ## ----eval = FALSE------------------------------------------------------------- # library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) ## ----------------------------------------------------------------------------- data(cpgtoy) head(cpg.pval, 20) ## ----------------------------------------------------------------------------- res1 = methylglm(cpg.pval = cpg.pval, minsize = 200, maxsize = 500, GS.type = "KEGG") head(res1, 15) ## ----eval=FALSE--------------------------------------------------------------- # res2 = methylRRA(cpg.pval = cpg.pval, method = "ORA", # minsize = 200, maxsize = 210) # head(res2, 15) ## ----eval=FALSE--------------------------------------------------------------- # res3 = methylRRA(cpg.pval = cpg.pval, method = "GSEA", # minsize = 200, maxsize = 210) # head(res3, 10) ## ----eval=FALSE--------------------------------------------------------------- # res4 = methylgometh(cpg.pval = cpg.pval, sig.cut = 0.001, # minsize = 200, maxsize = 210) # head(res4, 15) ## ----------------------------------------------------------------------------- data(GSlisttoy) ## to make the display compact, only a proportion of each gene set is shown head(lapply(GS.list, function(x) x[1:30]), 3) ## ----eval=FALSE--------------------------------------------------------------- # library(BiocParallel) # res_p = methylglm(cpg.pval = cpg.pval, minsize = 200, # maxsize = 500, GS.type = "KEGG", parallel = TRUE) ## ----------------------------------------------------------------------------- data(CpG2Genetoy) head(CpG2Gene) ## ----------------------------------------------------------------------------- FullAnnot = prepareAnnot(CpG2Gene) ## ----------------------------------------------------------------------------- GS.list = GS.list[1:10] res5 = methylRRA(cpg.pval = cpg.pval, FullAnnot = FullAnnot, method = "ORA", GS.list = GS.list, GS.idtype = "SYMBOL", minsize = 100, maxsize = 300) head(res5, 10) ## ----eval=FALSE--------------------------------------------------------------- # res6 = methylglm(cpg.pval = cpg.pval, array.type = "450K", # GS.type = "Reactome", minsize = 100, maxsize = 110) # head(res6, 10) ## ----------------------------------------------------------------------------- barplot(res1, num = 8, colorby = "pvalue") ## ----sessionInfo-------------------------------------------------------------- sessionInfo()