I've just tried it out with the current release version of R 3.4.2 and the GSEABase package (1.40.1) and it works fine. You need to update to the current R release version 3.4.2 and current release of Bioconductor; see http://bioconductor.org/install.
MSigDB <- getBroadS ...
... Assuming the downloaded file is called 'gwas_catalog_v1.0.1-associations_e90_r2017-09-12.tsv', what about
gwascat <- read.delim("gwas_catalog_v1.0.1-associations_e90_r2017-09-12.tsv", sep="\t", header=TRUE, stringsAsFactors=FALSE)
just look at the source code of 'makeCurrentGwascat()' and y ...
indeed, if you try to access the annotation of the gene with the 'genes()' method and its default parameters, you won't find it:
"8831" %in% names(genes(txdb))
however, the gene forms part of this annotation package and you can see it if you use the 'exonsBy()' method:
I want to build a table of counts using 'summarizeOverlaps()' from a PE RNA-seq data set generated with a strand-specific library preparation protocol from NewEngland Biolabs called "NEBNext Ultra Directional RNA Library Prep Kit for Illumina". The web page from that protocol says that it "util ...