snipar.gwas module

snipar.gwas.compute_batch_boundaries(snp_ids, batch_size)

snipar.gwas.compute_ses(alpha_cov)

snipar.gwas.fit_models(y, G)

snipar.gwas.outarray_effect(est, ses, freqs, vy)

snipar.gwas.process_batch(y, pedigree, tau, sigma2, snp_ids=None, bedfile=None, bgenfile=None, par_gts_f=None, parsum=False, fit_sib=False, max_missing=5, min_maf=0.01, verbose=False, print_sample_info=False)

snipar.gwas.process_chromosome(chrom_out, y, pedigree, tau, sigma2, outprefix, bedfile=None, bgenfile=None, par_gts_f=None, fit_sib=False, parsum=False, max_missing=5, min_maf=0.01, batch_size=10000, no_hdf5_out=False, no_txt_out=False)

snipar.gwas.transform_phenotype(inv_root, y, fam_indices, null_mean=None)

Transform phenotype based on inverse square root of phenotypic covariance matrix. If the null model included covariates, the fitted mean is removed rather than the overall mean

snipar.gwas.write_output(chrom, snp_ids, pos, alleles, outfile, parsum, sib, alpha, alpha_ses, alpha_cov, sigma2, tau, freqs)

Write fitted SNP effects and other parameters to output HDF5 file.

snipar.gwas.write_txt_output(chrom, snp_ids, pos, alleles, outfile, parsum, sib, alpha, alpha_cov, sigma2, tau, freqs)