[BioC] SomaticCancerAlterations:::.validate_maf, read_maf, maf2gr

Julian Gehring julian.gehring at embl.de
Tue Aug 12 18:17:45 CEST 2014

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

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
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