GSEABase::getBroadSets returns error with the latest MSigDB version
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Ezgi ▴ 60
@ezgi-24130
Last seen 2.1 years ago
United States

I recently downloaded a XML file of all the gene sets from MSigDB v7.2 from https://data.broadinstitute.org/gsea-msigdb/msigdb/release/7.2/msigdb_v7.2.xml.
When I try to import gene sets with GSEABase::getBroadSets I get an error:

curl::curl_download("https://data.broadinstitute.org/gsea-msigdb/msigdb/release/7.2/msigdb_v7.2.xml", "msigdb_v7.2.xml")
msigdb_gsets <- GSEABase::getBroadSets("msigdb_v7.2.xml")

Error: 'getBroadSets' failed to create gene sets:
  invalid BroadCollection category: 'c8'

When I try to import XML files from an older version (e.g. v5.2 -- which doesn't have the c8 category) I get no errors.
Is there a way to get around this?


sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
[1] GSEABase_1.52.0      graph_1.68.0         annotate_1.68.0      XML_3.99-0.5        
[5] AnnotationDbi_1.52.0 IRanges_2.24.0       S4Vectors_0.28.0     Biobase_2.50.0      
[9] BiocGenerics_0.36.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5     digest_0.6.25  R6_2.4.1       xtable_1.8-4   DBI_1.1.0     
 [6] RSQLite_2.2.1  httr_1.4.2     rlang_0.4.7    blob_1.2.1     vctrs_0.3.2   
[11] tools_4.0.2    bit64_4.0.5    bit_4.0.4      compiler_4.0.2 memoise_1.1.0
GSEABase • 1.0k views
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@martin-morgan-1513
Last seen 6 weeks ago
United States

Thanks for the report. The c8 (Cell Type Signatures) pathways have been added to version 1.52.1, which should be available after the next 'nightly' build, probably Saturday after about 2pm US Eastern. It can also be installed from GitHub for your version of R / Bioconductor with

BiocManager::install("Bioconductor/GSEABase", ref = "RELEASE_3_12")
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