Closed lightning-auriga closed 3 years ago
this is probably done, but I'll leave it open until I can test it once.
ooh new problem. so the component number is indeed increased, which is great. however, now the smallest platform/ancestry combinations (by sample count) cause smartpca to segfault. they're not beneath the theoretical limit of subjects needed for a 20 PC estimation. so this is probably some sort of quiet heuristic bound I've never run into before. the practical effect is that the Makefile.config
parameter SAMPLE_SIZE_MIN
must be increased a bit above the parameter SMARTPCA_N_PCS
.
i'm going to try SAMPLE_SIZE_MIN := 30
for plco and see what happens
I unceremoniously declare this handled. PC count is at 20, min sample size per platform/ancestry combo is 50. They are successfully estimated, and downstream methods (primarily construct.model.matrix
) intercept them correctly and add them.
I've started hearing rumors that the number of principal components used in association may be changed to some other number greater than the current 10. a nice gift to bequeath to my successor would be a configurable parameter for this somewhere in
Makefile.config
, and support for that increased ceiling in the model matrix constructor, such that they don't have to deal with an immediate extension buried within makefiles.