Question about joint analysis in Hail (hl.MatrixTable.union_cols)


#1

In your documentation on logistic regression https://hail.is/docs/0.2/methods/stats.html#hail.methods.logistic_regression_rows
you point to a very interesting article: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4049324/ (thanks for this by the way)

Given my cohorts, the best recommendation is a joint analysis using Firth test. The appropriate Hail function to join the datasets seems to be hl.MatrixTable.union_cols , is that right?

What happens when variants have an identical location in both sets to join, but have a different rsid?


#2

union_cols uses the MatrixTable row key to join. If both are keyed by locus and alleles, then that is the join key – the rsid from the right side will be ignored.

At some point we’ll add a full set of MatrixTable join methods, which will let you join the row fields as well.


#3

Perfect, thank you.