Some mutations aren't available

[gaiusjaugustus]

I have used the following code to download mutations for the COADREAD complete non-hypermutables.

mycgds <- CGDS("http://www.cbioportal.org/public-portal/") mycancerstudy <- "coadread_tcga_pub" mycaselist <- "coadread_tcga_pub_nonhypermut" mygeneticprofile <- "coadread_tcga_mutations" GeneList.APCKRASTP53 <- c("APC", "KRAS", "TP53") Mutations <- getProfileData(mycgds, GeneList.APCKRASTP53, mygeneticprofile, mycaselist)

I haven't had any trouble running cgdsr. However, I compared the samples to what was on cbioportal.org and realized there is a discrepancy.

Some samples have NaNs and other have NAs. When I look in cbioportal, these genes DO seem to have mutation data in those patients, but it isn't being downloaded.

For example: Sample TCGA.A6.2670 cgdsr: APC == NA cbioportal: APC Mutation: E1353*

Sample TCGA.AA.3524 cgdsr: APC == NaN cbioportal: APC Mutation: X215_splice

I'm not sure this is an issue with cgdsr, but just in case, I figured I'd open an issue about it.