Re: [Bioc-devel] expand,VCF and the AD geno field

2013-09-24 Thread Michael Lawrence
That's great, thanks. On Tue, Sep 24, 2013 at 12:16 PM, Valerie Obenchain wrote: > Michael, > > This is implemented in 1.7.48. AD is expanded as a list matrix where each > list element holds a REF,ALT pair. > > Val > > > > On 09/05/2013 07:36 AM, Valerie Obenchain wrote: > >> Hi, >> >> On 09/04/

Re: [Bioc-devel] expand,VCF and the AD geno field

2013-09-24 Thread Valerie Obenchain
Michael, This is implemented in 1.7.48. AD is expanded as a list matrix where each list element holds a REF,ALT pair. Val On 09/05/2013 07:36 AM, Valerie Obenchain wrote: Hi, On 09/04/2013 04:23 PM, Michael Lawrence wrote: Hi, Val, I just fixed expand,VCF to support multiple 'A' columns

Re: [Bioc-devel] expand,VCF and the AD geno field

2013-09-05 Thread Valerie Obenchain
Hi, On 09/04/2013 04:23 PM, Michael Lawrence wrote: Hi, Val, I just fixed expand,VCF to support multiple 'A' columns in info. Looks like expand,DataFrame does a cartesian product of list columns, which is not what we want in that case. Thanks. Ran up against another hurdle though: the conv

[Bioc-devel] expand,VCF and the AD geno field

2013-09-04 Thread Michael Lawrence
Hi, Val, I just fixed expand,VCF to support multiple 'A' columns in info. Looks like expand,DataFrame does a cartesian product of list columns, which is not what we want in that case. Ran up against another hurdle though: the conventional AD genotype field has a (virtual) Number of 'A+1', but sin