## ----echo = FALSE, message = FALSE-------------------------------------------- library(knitr) knitr::opts_chunk$set( error = FALSE, tidy = FALSE, message = FALSE, warning = FALSE, fig.align = "center") ## ----------------------------------------------------------------------------- library(rGREAT) ## ----------------------------------------------------------------------------- set.seed(123) gr = randomRegions(nr = 1000, genome = "hg19") head(gr) ## ----eval = FALSE------------------------------------------------------------- # job = submitGreatJob(gr) ## ----echo = FALSE------------------------------------------------------------- job = readRDS(system.file("extdata", "GreatJob.rds", package = "rGREAT")) ## ----------------------------------------------------------------------------- job ## ----eval = FALSE------------------------------------------------------------- # job = submitGreatJob(gr, species = "mm9") # of course, gr should be from mm9 # job = submitGreatJob(gr, adv_upstream = 10, adv_downstream = 2, adv_span = 2000) # job = submitGreatJob(gr, rule = "twoClosest", adv_twoDistance = 2000) # job = submitGreatJob(gr, rule = "oneClosest", adv_oneDistance = 2000) ## ----eval = FALSE------------------------------------------------------------- # job = submitGreatJob(gr, version = "3.0") # job = submitGreatJob(gr, version = "2.0") ## ----message = TRUE----------------------------------------------------------- tbl = getEnrichmentTables(job) names(tbl) tbl[[1]][1:2, ] ## ----------------------------------------------------------------------------- job ## ----eval = FALSE------------------------------------------------------------- # tbl = getEnrichmentTables(job, ontology = c("GO Molecular Function", "Human Phenotype")) # tbl = getEnrichmentTables(job, category = c("GO")) ## ----eval = FALSE------------------------------------------------------------- # tbl2 = getEnrichmentTables(job, download_by = "tsv") ## ----------------------------------------------------------------------------- availableOntologies(job) availableCategories(job) availableOntologies(job, category = "GO") ## ----fig.width = 6, fig.height = 6-------------------------------------------- plotVolcano(job, ontology = "GO Biological Process") ## ----fig.width = 10, fig.height = 10/3, fig.align = 'center'------------------ plotRegionGeneAssociations(job) ## ----------------------------------------------------------------------------- getRegionGeneAssociations(job) ## ----eval = FALSE------------------------------------------------------------- # plotRegionGeneAssociations(job, which_plot = 1) ## ----fig.width = 10, fig.height = 10/3---------------------------------------- plotRegionGeneAssociations(job, ontology = "GO Molecular Function", term_id = "GO:0004984") getRegionGeneAssociations(job, ontology = "GO Molecular Function", term_id = "GO:0004984") ## ----eval = FALSE------------------------------------------------------------- # shinyReport(job) ## ----------------------------------------------------------------------------- sessionInfo()