sample size for compute_r2

popgenmethods / pyrho

Fast inference of fine-scale recombination rates based on fused-LASSO

MIT License

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sample size for compute_r2 #16

Closed jarobin closed 4 years ago

jarobin commented 4 years ago

Should the sample size for compute_r2 be the number of (diploid) individuals or the number of haplotypes? The options for make_table and hyperparam specify haplotypes, but the samplesize option of compute_r2 says "Number of individuals for which to compute statistics. Must be less than or equal to the sample size in tablefile." The example suggests the value of --samplesize should be the same across all three functions, I just want to confirm.

jeffspence commented 4 years ago

Thanks for this! It's the number of haplotypes. I've made the documentation clearer in commit 5b8b340c7fd4fb90ef88f007d15b0ddb09590bd9.