## ----knitr.setup, echo=FALSE-------------------------------------------------- library(knitr) knitr::opts_chunk$set( echo = TRUE, warning=FALSE, message=FALSE, error = FALSE, tidy = FALSE, cache = TRUE) # rmarkdown::render("loading_genesets.Rmd") ## ----load1, eval=FALSE-------------------------------------------------------- # library(zenith) # # ## MSigDB as ENSEMBL genes # # all genesets in MSigDB # gs.msigdb = get_MSigDB() # # # only Hallmark gene sets # gs = get_MSigDB('H') # # # only C1 # gs = get_MSigDB('C1') # # # C1 and C2 # gs = get_MSigDB(c('C1', 'C2')) # # # C1 as gene SYMBOL # gs = get_MSigDB('C1', to="SYMBOL") # # # C1 as gene ENTREZ # gs = get_MSigDB('C1', to="ENTREZ") # # ## Gene Ontology # gs.go = get_GeneOntology() # # # load Biological Process and gene SYMBOL # gs.go = get_GeneOntology("BP", to="SYMBOL") ## ----load2, eval=FALSE-------------------------------------------------------- # library(EnrichmentBrowser) # # # KEGG # gs.kegg = getGenesets(org = "hsa", # db = "kegg", # gene.id.type = "ENSEMBL", # return.type = "GeneSetCollection") # # ## ENRICHR resource # # provides many additional gene set databases # df = showAvailableCollections( org = "hsa", db = "enrichr") # # head(df) # # # Allen_Brain_Atlas_10x_scRNA_2021 # gs.allen = getGenesets( org = "hsa", # db = "enrichr", # lib = "Allen_Brain_Atlas_10x_scRNA_2021", # gene.id.type = "ENSEMBL", # return.type = "GeneSetCollection") ## ----custom, eval=FALSE------------------------------------------------------- # # Load gene sets from GMT file # gmt.file <- system.file("extdata/hsa_kegg_gs.gmt", # package = "EnrichmentBrowser") # gs <- getGenesets(gmt.file)