## ----echo = FALSE, message = FALSE-------------------------------------------- library(knitr) knitr::opts_chunk$set( error = FALSE, tidy = FALSE, message = FALSE, warning = FALSE, fig.align = "center") ## ----------------------------------------------------------------------------- library(rGREAT) rGREAT:::BIOC_ANNO_PKGS$txdb ## ----eval = FALSE------------------------------------------------------------- # great(gr, "GO:BP", "galGal6") ## ----eval = FALSE------------------------------------------------------------- # great(gr, "GO:BP", "TxDb.Ggallus.UCSC.galGal6.refGene") ## ----eval = FALSE------------------------------------------------------------- # # Giant panda # great(gr, "GO:BP", biomart_dataset = "amelanoleuca_gene_ensembl") ## ----------------------------------------------------------------------------- library(msigdbr) msigdbr_species() ## ----------------------------------------------------------------------------- h_gene_sets = msigdbr(species = "chimpanzee", category = "H") head(h_gene_sets) ## ----------------------------------------------------------------------------- # convert to a list of gene sets h_gene_sets = split(h_gene_sets$entrez_gene, h_gene_sets$gs_name) h_gene_sets = lapply(h_gene_sets, as.character) # just to make sure gene IDs are all in character. h_gene_sets[1:2] ## ----eval = FALSE------------------------------------------------------------- # great(gr, h_gene_sets, "panTro6") ## ----eval = .Platform$OS.type == "unix"--------------------------------------- genes = getGenomeDataFromNCBI("GCF_011762595.1", return_granges = TRUE) genes ## ----eval = .Platform$OS.type == "unix"--------------------------------------- seqlengths(genes) ## ----eval = FALSE------------------------------------------------------------- # great(gr, your_go_gene_sets, tss_source = genes, ...) ## ----eval = .Platform$OS.type == "unix"--------------------------------------- lt = getGenomeDataFromNCBI("GCF_011762595.1", return_granges = FALSE) names(lt) ## ----eval = .Platform$OS.type == "unix"--------------------------------------- head(lt$genome) head(lt$gene) ## ----eval = .Platform$OS.type == "unix"--------------------------------------- map = structure(lt$genome$genbankAccession, names = lt$genome$refseqAccession) head(map) ## ----eval = .Platform$OS.type == "unix"--------------------------------------- genes = lt$gene genes[, 1] = map[ genes[, 1] ] genes = genes[!is.na(genes[, 1]), ] genes = GRanges(seqnames = genes[, 1], ranges = IRanges(genes[, 2], genes[, 3]), strand = genes[, 4], gene_id = genes[, 5]) ## ----eval = .Platform$OS.type == "unix"--------------------------------------- sl = structure(lt$genome$length, names = lt$genome$genbankAccession) sl = sl[!is.na(names(sl))] seqlengths(genes) = sl genes ## ----eval = FALSE------------------------------------------------------------- # great(gr, your_go_gene_sets, tss_source = genes, ...) ## ----------------------------------------------------------------------------- getKEGGGenome("mgp")