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extension for gs descriptions #23

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extension for gs descriptions #23

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8c60233
update msigdbr_collections()
ozturan Dec 7, 2022
e1dc111
update msigdbr-collections.R
ozturan Dec 7, 2022
ceead5c
update msigdbr_genesets
ozturan Dec 8, 2022
1839091
update
ozturan Dec 8, 2022
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update msigdbr_collections() 
add the major groups and their individual descriptions
@ozturan
ozturan authored Dec 7, 2022
commit 8c60233652fd2751cf5f1deca726b364c506ab37
37 changes: 34 additions & 3 deletions R/msigdbr-collections.R
View file
Original file line number Diff line number Diff line change
@@ -8,8 +8,39 @@
#' @examples
#' msigdbr_collections()
msigdbr_collections <- function() {
msigdbr_geneset_desc <- c("POSITIONAL GENE SETS",
"CHEMICAL AND GENETIC PERTURBATIONS",
"CANONICAL PATHWAYS",
"CANONICAL PATHWAYS - BIOCARTA",
"CANONICAL PATHWAYS - KEGG",
"CANONICAL PATHWAYS - PID",
"CANONICAL PATHWAYS - REACTOME",
"CANONICAL PATHWAYS - WIKIPATHWAYS",
"CURATED GENES SETS",
"MICRORNA TARGETS - LEGACY",
"MICRORNA TARGETS - MIR",
"TRANSCRIPTION FACTOR TARGETS - GTRD",
"TRANSCRIPTION FACTOR TARGETS - LEGACY",
"REGULATORY TARGET GENES",
"CANCER GENE NEIGHBOURHOODS",
"CANCER MODULES",
"COMPUTATIONAL GENE SETS",
"GENE ONTOLOGY - BIOLOGICAL PROCESS",
"GENE ONTOLOGY - CELLULAR COMPONENT",
"GENE ONTOLOGY - MOLECULAR FUNCTION",
"HUMAN PHENOTYPE ONTOLOGY",
"ONTOLOGY GENE SETS",
"ONCOGENIC SIGNATURE GENE SETS",
"IMMUNESIGDB",
"VACCINE RESPONSE GENE SETS",
"IMMUNOLOGIC SIGNATURE GENE SETS",
"CELL TYPE SIGNATURE GENE SETS",
"HALLMARK GENE SETS")
msigdbr_genesets %>%
distinct(.data$gs_cat, .data$gs_subcat, .data$gs_id) %>%
count(.data$gs_cat, .data$gs_subcat, name = "num_genesets") %>%
arrange(.data$gs_cat, .data$gs_subcat)
distinct(.data$gs_cat, .data$gs_subcat, .data$gs_id) %>%
count(.data$gs_cat, .data$gs_subcat, name = "num_genesets") %>%
arrange(.data$gs_cat, .data$gs_subcat) %>%
group_by(gs_cat) %>%
bind_rows(summarise_all(., ~if(is.numeric(.)) sum(.) else "")) %>%
unique() %>% arrange(gs_cat, desc=T) %>% cbind(msigdbr_geneset_desc)
}