Accessing particular gene set with msigdbr on R

Question

[Aryan]

I want to access specifically the gene set at https://www.gsea-msigdb.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_STEM_CELL using msigdbr on R 4.1.3.

However, I can only refer to gene sets using category and subcategory - but this fetches me thousands of gene sets, rather than the unique one that I want.

So, how can I get only the unique gene set above?

Answer 1

[mark.ziemann]

One way is to use grep on the msigdb tibble to select the gene sets that match the query:

> library("msigdbr")
> msigdb_gene_sets <-  msigdbr(species = "human")
> myset <- msigdb_gene_sets[grep("ivanova_hematopoiesis",msigdb_gene_sets$gs_name,ignore.case=TRUE),]

but that results in several matches

[1] "IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR"        
[2] "IVANOVA_HEMATOPOIESIS_INTERMEDIATE_PROGENITOR" 
[3] "IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR"         
[4] "IVANOVA_HEMATOPOIESIS_MATURE_CELL"             
[5] "IVANOVA_HEMATOPOIESIS_STEM_CELL"               
[6] "IVANOVA_HEMATOPOIESIS_STEM_CELL_AND_PROGENITOR"
[7] "IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM"     
[8] "IVANOVA_HEMATOPOIESIS_STEM_CELL_SHORT_TERM"

so the subset command can be used to get the exact gene set.

> myset <- subset(msigdb_gene_sets, gs_name=="IVANOVA_HEMATOPOIESIS_STEM_CELL")
> dim(myset)
[1] 208  15

[Jaber]

Could you please tell me how can I access inflammatory genes for certain organs to study like wanna study inflammatory genes in HCC, I just want to have inflammatory genes as a set