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individual-callrate different between check.marker and perid.summary?

Posted: Fri Sep 30, 2016 10:23 am
by TobiasW82
Hi,
this is a short question. When I perform perid.summary() on my gwaa.data-object, the resulting data frame tells me, that I have 4 individuals which have a callrate lower than 95%. In contrast, when I perform check.marker() and define the argument perid.callrate as 0.95, all individuals are hold in the analysis? Why this happens? I would guess, that check.marker() exclude the same individuals as found with perid.summary().

Thanks for your help in advance.

Best,
Tobi