Closed cristinaetrv closed 2 months ago
Computing p values accurately tailored to distribution that you'd expect if there is no spike - 6/6/24
We have merged the random matrix theory PR, which will be used and Ilha will be evaluating RMT works by setting the ratio of the number of covariates and sample size to a fixed value (p/n = c; c > 0) and letting both p and n go to infinity. This contrasts with classical statistical tests that fix p and let n go to infinity. We're going to evaluating whether RMT works better.
Seeing how well when we assume there is signal in the data, hypothesis test to detect spike in data - 6/6/24
Ilha is making progress on this. He is running first simulation now, running different combinations of singular value shrinkage estimators, and the different types of covariance matrix estimators, and he will be evaluating this via mean squared error on the poe effect estimators, that are simulated.
Conservativeness:
Austin will implement some spherical p-value tests that are a direct POIROT competitor
Test looks really successful at removing batch effects; TAMPOR does not appear to remove them, at least entirely.
Automatically launch PRS after ancestry from API server
Pushed back to last week of sprint
Display basic PRS results in webapp (table with individuals and their score) - @akotlar - 6/6/24 - https://github.com/bystrogenomics/bystro/pull/509
Same
Add batch processing for PRS C+T workflow with dosage matrix for memory issues
Under review
Need annotated AD stat summary to include ancestry
Done
Take in top hit from ancestry, convert to superpop, connect to LD map for corresponding pop for LD clump
Should be in testing by 6/6
Weigh PRS scores by gnomad allele frequencies for specific ancestries and the corresponding ancestry probability
Should be done by 6/6
Finish PRS-CS standard way without Langevin Dynamics
PR'd, there's a test to fix
Take in ancestry PCs as PRS-CS covariates
@akotlar and @austinTalbot7241993 will talk about this on Monday
Genotype imputation
Hypothesis testing
Guy at UC Davis has a good implementation, so we're relying on that
Covariance matrix estimation
We have geodisics in (may use in domain adaptation), we have pyreamann PR'd.
We have been working this week on how well the covariance matrix estimation, and conservativeness. Operator norm has the best MSE and worst conservativeness, and nuclear norm had the best conservativeness and ok MSE.
The difficulty is estimating the largest singular values, which needs to be done by looking at heterozygotes; we were shafting ourselves by looking at low frequency hets and with small effect sizes.
Will be done by 6/6 for prototype
On track, good progress
@akotlar
@cristinaetrv
@IlhaH
@austinTalbot7241993
Due date: June 6 2024
Documentation
Proteomics
PRS
Covariance Matrix Estimation/ML library Goal: Make more accurate predictions, more tailored test, better control false positive rate