## ---- echo = FALSE, message = FALSE-------------------------------------- library(knitr) knitr::opts_chunk$set( error = FALSE, tidy = FALSE, message = FALSE, fig.align = "center") options(width = 100) options(markdown.HTML.stylesheet = "custom.css") ## ---- echo = 2----------------------------------------------------------- suppressWarnings(suppressPackageStartupMessages(library(rGREAT))) library(rGREAT) ## ------------------------------------------------------------------------ set.seed(123) bed = circlize::generateRandomBed(nr = 1000, nc = 0) bed[1:2, ] ## ------------------------------------------------------------------------ job = submitGreatJob(bed) ## ------------------------------------------------------------------------ job ## ---- eval = FALSE------------------------------------------------------- ## job = submitGreatJob(bed, species = "mm9") ## job = submitGreatJob(bed, bg, species = "mm9") ## job = submitGreatJob(bed, adv_upstream = 10, adv_downstream = 2, adv_span = 2000) ## job = submitGreatJob(bed, rule = "twoClosest", adv_twoDistance = 2000) ## job = submitGreatJob(bed, rule = "oneClosest", adv_oneDistance = 2000) ## ---- eval = FALSE------------------------------------------------------- ## job = submitGreatJob(bed, version = "3.0") ## job = submitGreatJob(bed, version = "2.0") ## ------------------------------------------------------------------------ tb = getEnrichmentTables(job) names(tb) tb[[1]][1:2, ] ## ------------------------------------------------------------------------ job ## ---- eval = FALSE------------------------------------------------------- ## tb = getEnrichmentTables(job, ontology = c("GO Molecular Function", "BioCyc Pathway")) ## tb = getEnrichmentTables(job, category = c("GO")) ## ------------------------------------------------------------------------ availableOntologies(job) availableCategories(job) availableOntologies(job, category = "Pathway Data") ## ---- fig.width = 12, fig.height = 4, fig.align = 'center'--------------- par(mfrow = c(1, 3)) res = plotRegionGeneAssociationGraphs(job) res[1:2, ] ## ---- eval = FALSE------------------------------------------------------- ## plotRegionGeneAssociationGraphs(job, type = 1) ## ---- fig.width = 12, fig.height = 4------------------------------------- par(mfrow = c(1, 3)) res = plotRegionGeneAssociationGraphs(job, ontology = "GO Molecular Function", termID = "GO:0004984") res[1:2, ] ## ------------------------------------------------------------------------ sessionInfo()