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zhengxwen / SNPRelate

R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)
http://www.bioconductor.org/packages/SNPRelate
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Does snpgdsLDpruning calculate squared correlation coefficient? #42

Closed wvictor14 closed 6 years ago

wvictor14 commented 6 years ago

Hi,

Quick question, does snpgdsLDpruning calculate squared correlation coefficient or the correlation coefficient? I'm guessing the former but I'm not sure based on the description of the help file.

Thanks, Victor

zhengxwen commented 6 years ago

It is the correlation coefficient. When you run snpgdsLDpruning(), it shows:

    |LD| threshold: 0.2

indicating the LD value could be negative, so it is correlation coefficient.