Closed abought closed 5 years ago
Burden and SKAT tests are returning the same results as with previous rm.js versions.
However, the VT test presently fails in the demo region when running all possible masks + tests + LDL as phenotype: it tries to access cov[3][3]
, which is out of bounds for the 3x3 covariance matrix of input data.
Line with error: https://github.com/abought/raremetal.js/blob/f4b715011245be88b6dd677b26c218df2b89db03/src/app/stats.js#L206
lz-aggregation-tests.min.js? [sm]:149 TypeError: Cannot read property '3' of undefined
at get_conditional_dist (stats.js:206)
at calculate_mvt_pvalue (stats.js:275)
at stats.js:494
A version of the integration is available here: https://abought.github.io/locuszoom/examples/aggregation_tests.html?chrom=19&start=45312079&end=45512079
As of this writing there are run bugs with VT, and under rare conditions memory usage issues with SKATO. (I am working on resolving the latter)
Below is some information about the VT error for debugging, per @welchr request.
TypeError: Cannot read property '3' of undefined at get_conditional_dist (stats.js:206) at calculate_mvt_pvalue (stats.js:275) at stats.js:494
It seems to be trying to read element indices larger than the actual provided covariance matrix.
var scores = [0, 0, 0, 1.5462063784800575, 0.21031859503159187, 9.04952262687792]`
var cov = [[1,0.47234514133873046,0.3847563633178216],[0.47234514133873046,1,0.4872017342012682],[0.3847563633178216,0.4872017342012682,1]]
var comb = [0, 3]
Closing in favor of changes merged to develop.
🦑 Companion to, and must be merged after: https://github.com/statgen/raremetal.js/pull/9
Purpose
The new raremetal.js will make some changes to support additional aggregation tests.
This updates the LocusZoom demo with WIP support for two new tests (SKAT-O and VT), as well as updating the code to work with incoming rm.js API changes.