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.
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 haveNAs. 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.