Linkage Disequilibrium in SAS/Genetics

[MajaFerencakovic]

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

[SteveDenham · Accepted solution]

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

[MajaFerencakovic]

Yes,

that looks OK.

Thank you for your help