## ----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") ## ----------------------------------------------------------------------------- res = great(gr, "MSigDB:H", "txdb:hg19") res ## ----eval = FALSE------------------------------------------------------------- # great(gr, "GO:BP", "hg19") # great(gr, "GO:BP", "TxDb.Hsapiens.UCSC.hg19.knownGene") # great(gr, "GO:BP", "RefSeq:hg19") # great(gr, "GO:BP", "GREAT:hg19") # great(gr, "GO:BP", "Gencode_v19") ## ----------------------------------------------------------------------------- gs = read_gmt(url("http://dsigdb.tanlab.org/Downloads/D2_LINCS.gmt"), from = "SYMBOL", to = "ENTREZ", orgdb = "org.Hs.eg.db") gs[1:2] great(gr, gs, "hg19") ## ----------------------------------------------------------------------------- df = read.table(url("https://jokergoo.github.io/rGREAT_suppl/data/GREATv4.genes.hg19.tsv")) # note there must be a 'gene_id' column tss = GRanges(seqnames = df[, 2], ranges = IRanges(df[, 3], df[, 3]), strand = df[, 4], gene_id = df[, 5]) head(tss) ## ----------------------------------------------------------------------------- et = extendTSS(tss, genome = "hg19", gene_id_type = "SYMBOL") great(gr, "msigdb:h", extended_tss = et) ## ----eval = FALSE------------------------------------------------------------- # great(gr, gs, tss) # tss has a `gene_id` meta column ## ----------------------------------------------------------------------------- library(TxDb.Hsapiens.UCSC.hg19.knownGene) gene = genes(TxDb.Hsapiens.UCSC.hg19.knownGene) gene = gene[seqnames(gene) %in% paste0("chr", c(1:22, "X", "Y"))] head(gene) gl = seqlengths(gene)[paste0("chr", c(1:22, "X", "Y"))] # restrict to normal chromosomes head(gl) ## ----------------------------------------------------------------------------- et = extendTSS(gene, gl) head(et) ## ----------------------------------------------------------------------------- great(gr, gene_sets = gs, extended_tss = et) ## ----eval = FALSE------------------------------------------------------------- # gap = getGapFromUCSC("hg19", paste0("chr", c(1:22, "X", "Y"))) # great(gr, "MSigDB:H", "hg19", exclude = gap) ## ----eval = FALSE------------------------------------------------------------- # great(gr, "GO:BP", background = paste0("chr", 1:22)) # great(gr, "GO:BP", exclude = c("chrX", "chrY")) ## ----------------------------------------------------------------------------- tb = getEnrichmentTable(res) head(tb) ## ----fig.width = 6, fig.height = 6-------------------------------------------- plotVolcano(res) ## ----fig.width = 10, fig.height = 10/3, fig.align = 'center'------------------ plotRegionGeneAssociations(res) getRegionGeneAssociations(res) ## ----fig.width = 10, fig.height = 10/3, fig.align = 'center'------------------ plotRegionGeneAssociations(res, term_id = "HALLMARK_APOPTOSIS") getRegionGeneAssociations(res, term_id = "HALLMARK_APOPTOSIS") ## ----eval = FALSE------------------------------------------------------------- # shinyReport(res) ## ----------------------------------------------------------------------------- sessionInfo()