def test_skat(self):
ds2 = hl.import_vcf(resource('sample2.vcf'))
covariatesSkat = (hl.import_table(resource("skat.cov"), impute=True)
.key_by("Sample"))
phenotypesSkat = (hl.import_table(resource("skat.pheno"),
types={"Pheno": hl.tfloat64},
missing="0")
.key_by("Sample"))
intervalsSkat = (hl.import_locus_intervals(resource("skat.interval_list")))
weightsSkat = (hl.import_table(resource("skat.weights"),
types={"locus": hl.tlocus(),
"weight": hl.tfloat64})
.key_by("locus"))
ds = hl.split_multi_hts(ds2)
ds = ds.annotate_rows(gene=intervalsSkat[ds.locus],
weight=weightsSkat[ds.locus].weight)
ds = ds.annotate_cols(pheno=phenotypesSkat[ds.s].Pheno,
cov=covariatesSkat[ds.s])
ds = ds.annotate_cols(pheno=hl.cond(ds.pheno == 1.0,
False,
hl.cond(ds.pheno == 2.0,
True,
hl.null(hl.tbool))))
hl.skat(ds,
key_expr=ds.gene,
weight_expr=ds.weight,
y=ds.pheno,
x=ds.GT.n_alt_alleles(),
covariates=[ds.cov.Cov1, ds.cov.Cov2],
logistic=False).count()
hl.skat(ds,
key_expr=ds.gene,
weight_expr=ds.weight,
y=ds.pheno,
x=hl.pl_dosage(ds.PL),
covariates=[ds.cov.Cov1, ds.cov.Cov2],
logistic=True).count()
def matrix_table_array_arithmetic(mt_path):
mt = hl.read_matrix_table(mt_path)
mt = mt.filter_rows(mt.alleles.length() == 2)
mt.select_entries(
dosage=hl.pl_dosage(mt.PL)).select_rows()._force_count_rows()
def matrix_table_array_arithmetic():
mt = hl.read_matrix_table(resource('profile.mt'))
mt = mt.filter_rows(mt.alleles.length() == 2)
mt.select_entries(dosage = hl.pl_dosage(mt.PL)).select_rows()._force_count_rows()