| Title: | MSigDB Data Frame |
|---|---|
| Description: | Provides the Molecular Signatures Database (MSigDB) gene sets (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>, Liberzon et al. 2015 <doi:10.1016/j.cels.2015.12.004>, Castanza et al. 2023 <doi:10.1038/s41592-023-02014-7>) in an R data frame. Serves as the data source for 'msigdbr' <doi:10.32614/CRAN.package.msigdbr> (split into a separate package due to CRAN size restrictions). |
| Authors: | Igor Dolgalev [aut, cre] |
| Maintainer: | Igor Dolgalev <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 24.1.0 |
| Built: | 2025-03-09 05:57:49 UTC |
| Source: | https://github.com/igordot/msigdbdf |
Simplify the table of Ensembl gene ID mappings provided by MSigDB. MSigDB provides a CHIP file with canonical Ensembl IDs for each gene, but there are some genes with many (over ten) IDs. This function additionally reduces the number of multi-mapping IDs based on those actually appearing in MSigDB.
ensembl_genes(x)ensembl_genes(x)
x |
A list of data frames returned by |
A data frame with gene symbols and Ensembl IDs.
Convert the tables derived from the MSigDB SQLite database to a single table of gene set information. The output includes the full name, description, source publication, and other details for each gene set.
gene_set_details(x)gene_set_details(x)
x |
A list of data frames returned by |
A data frame with gene set details.
Convert the tables derived from the MSigDB SQLite database to a single table of member genes belonging to each gene set. The output includes gene symbols, NCBI (formerly Entrez) IDs, and Ensembl IDs for each gene set.
gene_set_members(x)gene_set_members(x)
x |
A list of data frames returned by |
A data frame with genes belonging to each gene set.
Download the Ensembl gene ID mappings compiled for MSigDB.
msigdb_ensembl(x)msigdb_ensembl(x)
x |
A list of data frames returned by |
MSigDB versions and the corresponding Ensembl releases for gene annotation:
2023.1 - 109 (February 2023)
2023.2 - 110 (July 2023)
2024.1 - 112 (May 2024)
A data frame with Ensembl gene IDs.
Download the MSigDB SQLite database and extract the relevant tables as data frames. Each database file holds one MSigDB release for one resource (human or mouse).
msigdb_sqlite(x)msigdb_sqlite(x)
x |
MSigDB version, such as |
A list of data frames.
MSigDB SQLite database documentation: https://docs.gsea-msigdb.org/#MSigDB/MSigDB_SQLite_Database/
Retrieve a data frame of MSigDB gene sets and their member genes.
Starting with release 2022.1, MSigDB was split into human and mouse resources, each one provided in the approved gene symbols of its respective species.
The MSigDB versioning convention is in the format Year.Release.Species.
The species referenced in this function is the one specified in the release version.
msigdbdf(target_species = c("HS", "MM"))msigdbdf(target_species = c("HS", "MM"))
target_species |
Species abbreviation for human or mouse databases ( |
A tibble (a data frame with class tibble::tbl_df) of gene sets with one gene per row.
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci. 2005 Oct 25;102(43):15545-50. doi:10.1073/pnas.0506580102
Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 2015 Dec 23;1(6):417-425. doi:10.1016/j.cels.2015.12.004
Castanza AS, Recla JM, Eby D, Thorvaldsdóttir H, Bult CJ, Mesirov JP. Extending support for mouse data in the Molecular Signatures Database (MSigDB). Nat Methods. 2023 Nov;20(11):1619-1620. doi:10.1038/s41592-023-02014-7