getMsigdbGenesets.RdgetMsigdbGenesets
getMsigdbGenesets(msigCollection, species)
| msigCollection | data.frema with columns gs_cat, gs_subcat |
|---|---|
| species | e.g. "Homo sapiens" |
Other fgsea:
fgsea_leading_edge_too_char(),
fgsea_msigdb_collections(),
fgsea_msigdb(),
fgsea_rank_contrasts(),
fgsea_rank(),
run_fgsea_for_allContrasts(),
run_fgsea_for_allGeneSets()
library(tidyverse) #> -- Attaching packages --------------------------------------- tidyverse 1.3.1 -- #> v ggplot2 3.3.5 v purrr 0.3.4 #> v tibble 3.1.4 v dplyr 1.0.7 #> v tidyr 1.1.3 v stringr 1.4.0 #> v readr 2.0.1 v forcats 0.5.1 #> -- Conflicts ------------------------------------------ tidyverse_conflicts() -- #> x dplyr::collapse() masks IRanges::collapse() #> x dplyr::combine() masks Biobase::combine(), BiocGenerics::combine() #> x dplyr::desc() masks IRanges::desc() #> x tidyr::expand() masks S4Vectors::expand() #> x dplyr::filter() masks stats::filter() #> x dplyr::first() masks S4Vectors::first() #> x dplyr::lag() masks stats::lag() #> x ggplot2::Position() masks BiocGenerics::Position(), base::Position() #> x purrr::reduce() masks IRanges::reduce() #> x dplyr::rename() masks S4Vectors::rename() #> x dplyr::select() masks AnnotationDbi::select() #> x dplyr::slice() masks IRanges::slice() library(msigdbr) msigdbr::msigdbr_species() #> # A tibble: 20 x 2 #> species_name species_common_name #> <chr> <chr> #> 1 Anolis carolinensis Carolina anole, green anole #> 2 Bos taurus bovine, cattle, cow, dairy cow, domestic cat~ #> 3 Caenorhabditis elegans roundworm #> 4 Canis lupus familiaris dog, dogs #> 5 Danio rerio leopard danio, zebra danio, zebra fish, zebr~ #> 6 Drosophila melanogaster fruit fly #> 7 Equus caballus domestic horse, equine, horse #> 8 Felis catus cat, cats, domestic cat #> 9 Gallus gallus bantam, chicken, chickens, Gallus domesticus #> 10 Homo sapiens human #> 11 Macaca mulatta rhesus macaque, rhesus macaques, Rhesus monk~ #> 12 Monodelphis domestica gray short-tailed opossum #> 13 Mus musculus house mouse, mouse #> 14 Ornithorhynchus anatinus duck-billed platypus, duckbill platypus, pla~ #> 15 Pan troglodytes chimpanzee #> 16 Rattus norvegicus brown rat, Norway rat, rat, rats #> 17 Saccharomyces cerevisiae baker's yeast, brewer's yeast, S. cerevisiae #> 18 Schizosaccharomyces pombe 972h- NA #> 19 Sus scrofa pig, pigs, swine, wild boar #> 20 Xenopus tropicalis tropical clawed frog, western clawed frog species <- "Homo sapiens" species <- "Mus musculus" hallmark <- msigdbr_collections() %>% filter(.data$gs_cat == "H") #hallmark$gs_subcat <- "HALLMARK" C5 <- bind_rows( {msigdbr_collections() %>% filter(.data$gs_cat == "C5") %>% filter(grepl("^GO:", .data$gs_subcat))}, hallmark, {msigdbr_collections() %>% filter(.data$gs_subcat == "CP:KEGG")} ) C5 #> # A tibble: 5 x 3 #> gs_cat gs_subcat num_genesets #> <chr> <chr> <int> #> 1 C5 "GO:BP" 7481 #> 2 C5 "GO:CC" 996 #> 3 C5 "GO:MF" 1708 #> 4 H "" 50 #> 5 C2 "CP:KEGG" 186 fgseaGSlist <- prora::getMsigdbGenesets(C5, species)