使用R语言获取特定关键词的通路 （msigdb数据库）

https://www.gsea-msigdb.org/gsea/msigdb

 CGP     CP:BIOCARTA         CP:KEGG     CP:REACTOME    CP:WIKIPATHWAYS

# get all human gene sets

msigdbr(species = "Homo sapiens")
# get mouse C2 (curated) CGP (chemical and genetic perturbations) gene sets

msigdbr(species = "Mus musculus", category = "C2", subcategory = "CGP")

https://www.gsea-msigdb.org/gsea/msigdb/mouse/genesets.jsp?collection=CP

.libPaths(c("/home/data/t040413/R/x86_64-pc-linux-gnu-library/4.2",
            "/home/data/t040413/R/yll/usr/local/lib/R/site-library",
            "/refdir/Rlib/",   "/usr/local/lib/R/library"))



#request 2
.libPaths(c( "/home/data/t040413/R/x86_64-pc-linux-gnu-library/4.2",
             "/home/data/t040413/R/yll/usr/local/lib/R/site-library",  
             "/refdir/Rlib/", "/usr/local/lib/R/library"))

library(GO.db)
library(Seurat)
library(dplyr)
library(tibble)
library(readr)

getOption("repos");help("repositories", package =
                          "BiocManager")

#BiocManager::install('msigdb',site_repository = 'https://cran.rstudio.com/' )
library(msigdb)

#如果直接使用category = "C2",subcategory = "CP"提前相应的数据集里面的基因集容易忽略一些数据，所以建议只使用category参数，不使用subcategory

#6提取并制备人的hallmarks列表---------
msigdbr::msigdbr_collections()
all_gene_sets_hs = msigdbr::msigdbr(species = "Mus musculus",category = "C2",subcategory = "CP") #Mus musculus  Homo sapiens
#saveRDS(all_gene_sets_hs,file="~/datasets/all_gene_sets_hs_msigdb.rds")
all_gene_sets_hs = msigdbr::msigdbr(species = "Mus musculus",category = "C2") #Mus musculus  Homo sapiens

all_gene_sets_hs 
table(all_gene_sets_hs$gs_subcat)

#假设我们这里想要寻找的是APOPTOSIS相关通路

#pattern参数内输入想要寻找的关键词，这里用的是"APOPTOSIS"

h2 <- all_gene_sets_hs[grep(pattern = "APOPTOSIS",x = all_gene_sets_hs$gs_name,ignore.case = TRUE),]

length(unique(h2$gs_name))#查看唯一通路

length(unique(h2$human_gene_symbol))#查看所有通路中的唯一基因
length(unique(h2$gene_symbol))#查看所有通路中的唯一基因
table(h2$gs_subcat)
table(h2$gs_name)

write.csv(h2,"allPathway_apoptosis.csv")#保存结果 
h2
h2_list=split(x = h2$gene_symbol,f=h2$gs_name )
h2_list

https://www.gsea-msigdb.org/gsea/msigdb/human/search.jsp