attachContext errored out

[jianxinwang]

Hi,

I'm having trouble with this code:

> x <- attachContext(mutData = x,
+                    chr_colName = "chr",
+                    start_colName = "position",
+                    end_colName = "position",
+                    nucl_contextN = 3,
+                    BSGenomeDb = hg38)
An error has occurred!

I traced down the place and found the following is causing the failure:

if ((! "BSgenome" %in% class(BSGenomeDb))  | 
      sum(c("pkgname", "organism") %in% methods::slotNames(BSGenomeDb)) != 2)
    stop ("Please, provide a valid 'BSgenome'-class object")

It turns out that "organism" is not in methods::slotNames(BSGenomeDb).

Please suggest solutions.

Thanks.

[jianxinwang]

I got the problem solved so I would like to post the solution. It turned out that installing mutSignature with this line solved the problem:

devtools::install_github("dami82/mutSignatures", force = TRUE, build_vignettes = FALSE)

So the package in Bioconductor remains to be updated.