Load keyword genesets for a specific species

Load keyword genesets for a specific species

load_keyword_genesets(taxon_id = 9606, category = NULL, as_table = FALSE)

Arguments

taxon_id

The taxon ID. To make it more flexible, you can also provide the Latin name or the normal name of the species.

category

Category of keywords. There are the following categories: "Biological process", "Cellular component", "Coding sequence diversity", "Developmental stage", "Disease", "Domain", "Ligand", "Molecular function", "Post-translational modification", "Technical term".

as_table

If true, the returned value will be a two-column data frame.

Details

Following are the supported species (with more than 1000 genes annotated):

  • "10090": Mus musculus / house mouse

  • "10116": Rattus norvegicus / Norway rat

  • "208964": Pseudomonas aeruginosa PAO1 / strain, g-proteobacteria

  • "224308": Bacillus subtilis subsp. subtilis str. 168 / strain, firmicutes

  • "237561": Candida albicans SC5314 / strain, budding yeasts

  • "243232": Methanocaldococcus jannaschii DSM 2661 / strain, euryarchaeotes

  • "284812": Schizosaccharomyces pombe 972h- / strain, ascomycete fungi

  • "3702": Arabidopsis thaliana / thale cress

  • "39947": Oryza sativa Japonica Group / (Japanese rice), monocots

  • "44689": Dictyostelium discoideum / species, cellular slime molds

  • "559292": Saccharomyces cerevisiae S288C / strain, budding yeasts

  • "6239": Caenorhabditis elegans / species, nematodes

  • "623": Shigella flexneri / species, enterobacteria

  • "7227": Drosophila melanogaster / (fruit fly), species, flies

  • "7955": Danio rerio / (zebrafish), species, bony fishes

  • "83332": Mycobacterium tuberculosis H37Rv / strain, high G+C Gram-positive bacteria

  • "83333": Escherichia coli K-12 / strain, enterobacteria

  • "83334": Escherichia coli O157:H7 / serotype, enterobacteria

  • "8355": Xenopus laevis / (African clawed frog), species, frogs & toads

  • "8364": Xenopus tropicalis / (tropical clawed frog), species, frogs & toads

  • "9031": Gallus gallus / (chicken), species, birds

  • "9601": Pongo abelii / (Sumatran orangutan), species, primates

  • "9606": Homo sapiens / human

  • "9823": Sus scrofa / (pig), species, even-toed ungulates

  • "9913": Bos taurus / cattle

  • "99287": Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 / strain, enterobacteria

Value

If as_table is set to FALSE, it returns a list of gene sets where Entrez IDs are the gene IDs. If as_table is set to TRUE, it returns a two-column data frame.

Examples

lt = load_keyword_genesets(9606)
lt[3:4]
#> $`3Fe-4S`
#> [1] "6390"
#> 
#> $`4Fe-4S`
#>  [1] "6059"   "48"     "50"     "54901"  "64428"  "51654"  "57019"  "1663"  
#>  [9] "1763"   "5424"   "5426"   "1806"   "55140"  "2068"   "2110"   "64789" 
#> [17] "83990"  "3658"   "11019"  "4337"   "4595"   "4719"   "4720"   "374291"
#> [25] "4728"   "4723"   "4682"   "10101"  "5558"   "5471"   "5980"   "55316" 
#> [33] "91543"  "51750"  "6390"   "441250" "55253" 
#> 
tb = load_keyword_genesets(9606, as_table = TRUE)
head(tb)
#>   keyword   gene
#> 1  2Fe-2S   2230
#> 2  2Fe-2S 150209
#> 3  2Fe-2S    316
#> 4  2Fe-2S  55847
#> 5  2Fe-2S 493856
#> 6  2Fe-2S 284106
# load_keyword_genesets("mouse")