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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).
The text was updated successfully, but these errors were encountered:
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)
.The text was updated successfully, but these errors were encountered: