getMsigdbGenesets: getMsigdbGenesets

In protViz/fgczgseaora: ORA, sigORA and GSEA functionalities for proteomic data

Description

getMsigdbGenesets

Usage

getMsigdbGenesets(msigCollection, species)

Arguments

msigCollection	data.frema with columns gs_cat, gs_subcat
species	e.g. "Homo sapiens"

See Also

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()

Examples

library(tidyverse)
library(msigdbr)
msigdbr::msigdbr_species()
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
fgseaGSlist <- prora::getMsigdbGenesets(C5, species)

protViz/fgczgseaora documentation built on Dec. 14, 2021, 9:22 p.m.