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Linkage Disequilibrium in SAS/Genetics

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Linkage Disequilibrium in SAS/Genetics

Hello to all! Smiley Happy

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


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‎03-17-2014 10:29 AM
Respected Advisor
Posts: 2,655

Re: Linkage Disequilibrium in SAS/Genetics

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

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‎03-17-2014 10:29 AM
Respected Advisor
Posts: 2,655

Re: Linkage Disequilibrium in SAS/Genetics

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

Contributor
Posts: 40

Re: Linkage Disequilibrium in SAS/Genetics

Yes,

that looks OK.

Thank you for your help Smiley Happy

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