Hi Using the package SomaticCancerAlterations, I am trying to read an updated version of tcga mutation data. From previous emails, I see you have the functions below to read/validate these data but I was wondering which seqinfo object do you use when calling the function maf2gr myMaf<-SomaticCancerAlterations:::.read_maf("myTCGAfile.maf") SomaticCancerAlterations:::.validate_maf(myMaf, seqinfo) myGr<-SomaticCancerAlterations:::.maf2gr(myMaf, seqinfo) thanks aedin

Hi Aedin, For the package, I have been using the information from the 1000genome reference (hs37d5). If you are only interested in the allosomes and autosomes (not the mitchondrium or any additional sequences), the seqinfo from hg19 give you the same seqlengths. You can get this from the BSgenome.Hsapiens.UCSC.hg19 in bioconductor, but would have to convert the seqnames first. Best wishes Julian On 12.08.2014 05:06, Aedin Culhane wrote: > Hi > Using the package SomaticCancerAlterations, I am trying to read an > updated version of tcga mutation data. From previous emails, I see you > have the functions below to read/validate these data but I was wondering > which seqinfo object do you use when calling the function maf2gr > > myMaf<-SomaticCancerAlterations:::.read_maf("myTCGAfile.maf") > SomaticCancerAlterations:::.validate_maf(myMaf, seqinfo) > myGr<-SomaticCancerAlterations:::.maf2gr(myMaf, seqinfo) > > thanks > aedin > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >