topic Re: Linkage Disequilibrium in SAS/Genetics in SAS Procedures

Linkage Disequilibrium in SAS/Genetics

MajaFerencakovic — Mon, 17 Mar 2014 12:43:29 GMT

Hello to all!

Today I started some serious work in SAS/Genetics and found a problem :smileyconfused:

I would like to get composite LD correlation matrix or at least table then I will find a way to create matrix from it (probably will post another question here).

So I am interested in Composite LD which can be obtained using proc allele with haplo = none or nonhwd. Later on I must perform PCA on this matrix...

Does anyone knows how to get LD values in sas table or matrix as output when using proc allele???

Thanks in advance!

Maja

Re: Linkage Disequilibrium in SAS/Genetics

SteveDenham — Mon, 17 Mar 2014 14:29:17 GMT

ODS OUTPUT is probably what you will need. If you specify any of the options

CORRCOEFF, DELTA, DPRIME, PROPDIFF, RHO, or YULESQ

then using

ods output ldmeasures=ldmeasures;

will give a dataset with the results I think you are looking for.

Steve Denham

Re: Linkage Disequilibrium in SAS/Genetics

MajaFerencakovic — Mon, 17 Mar 2014 16:15:03 GMT

Yes,

that looks OK.

Thank you for your help