Skat_table qq-plot


#1

It seems to be not further possible to
submit ‘skat_table.p_value’ to hl.plot.qq.

I received the following error message.

skat_table = hl.skat(key_expr=burden_ds.gene,
weight_expr=burden_ds.weight,
logistic=True,
y=burden_ds.caco,
x=burden_ds.GT.n_alt_alleles(),
covariates=[1])

In [43]: type(skat_table)
Out[43]: hail.table.Table

p = hl.plot.qq(skat_table.p_value)

AttributeError: Table instance has no field, method, or property ‘select_rows’
Did you mean:
Table methods: ‘select_globals’, ‘select’


#2

I see the issue. That plot methods assume the expression is on a matrix table, rather than a matrix table or table. I’ll fix it, but in the meantime, you can promote skat_table to a matrix table with hl.MatrixTable.from_rows_table first.

update: here’s the PR: https://github.com/hail-is/hail/pull/4176