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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
