Is There A Rare Variant Burden Test That Corrects For Gene Length?

Question

[joaofadista]

Hi,

I would like to know if any of the gene rare variant burden tests out there tries to correct for gene length, or number of variants per gene. As far as I know (might be wrong) this doesn´t seem to be implemented in any test. This would lead to always favor significant results for longer genes vs. shorter genes.

Best regards, João

[joaofadista]

Thanks for the tip. I will test it out!

[joaofadista]

Sorry, but your script does not work if you have less probes per gene.

Let say, substitute your:

n_probes = c(10, 20, 30, 50, 100, 250)

by:

n_probes = c(2, 5, 10, 20, 50, 100)

[Istvan Albert]

please don't keep adding answers to your question, use the 'comment' link to comment on an answer

Answer 1

[brentp]

I tried this with the CMC test to see if using more probes would change the p-value distribution of randomly generated data (no real signal)

It doesn't look like there's an increase in low p-values after increasing the number of probes in fact it's quite the opposite.

The code is this

so you can test other burden tests thanks to the AssotesteR package.

[Quak]

can you provide a path to the R package ?! google does not know it ! (probably it is misspelled)