snipar.gwas module

snipar.gwas.compute_batch_boundaries(snp_ids, batch_size)

snipar.gwas.find_common_ind_ids(obsfiles, impfiles, pheno_ids, from_chr=None, covar=None, keep=None, include_unrel=False)

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

snipar.gwas.process_batch(snp_ids, ped, n_vararr, imp_fams, pheno_ids=None, bedfile=None, bgenfile=None, par_gts_f=None, parsum=False, fit_sib=False, sib_diff=False, max_missing=5, min_maf=0.01, verbose=False, print_sample_info=False, impute_unrel=False, standard_gwas=False, robust=False, trios_sibs=False, add_jitter=False)

snipar.gwas.process_chromosome(chrom_out, y, varcomp_lst, ped, imp_fams, sigmas, outprefix, covariates=None, bedfile=None, bgenfile=None, par_gts_f=None, fit_sib=False, sib_diff=False, parsum=False, impute_unrel=False, max_missing=5, min_maf=0.01, batch_size=10000, no_hdf5_out=False, no_txt_out=False, cpus=1, debug=False, robust=False, trios_sibs=False, trios_only=False, add_jitter=False, standard_gwas=False)

snipar.gwas.split_batches(nsnp, niid, nbytes, num_cpus, parsum=False, sib=False)

snipar.gwas.write_output(chrom, snp_ids, pos, alleles, outfile, parsum, sib, sib_diff, alpha, alpha_ses, alpha_cov, sigmas, freqs, robust=False, standard_gwas=False, trios_sibs=False, trios_only=False)

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

snipar.gwas.write_txt_output(chrom, snp_ids, pos, alleles, outfile, parsum, sib, sib_diff, alpha, alpha_cov, sigmas, freqs, robust=False, standard_gwas=False, trios_sibs=False, trios_only=False)