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Confusing center stot in flashpca. #26

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privefl opened this issue May 10, 2017 · 0 comments
Open

Confusing center stot in flashpca. #26

privefl opened this issue May 10, 2017 · 0 comments

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@privefl
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privefl commented May 10, 2017

When using flashpca from the R package on PLINK files, it returns a list.
In this list, the slot center is confusing for me.
It seems that it returns twice the minor allele frequency whereas I thought it would return the column (SNP) means of the genotype matrix.
In the case that 2s are not coding for the minor allele (more 2s than 0s), these values are different: the column means are then 2 * (1 - MAF).

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