A low number of iterations in fastmode decreases accuracy
Nobody has claimed this yet.
- Dominant language
- C
- Stars
- 207
- Forks
- 61
- PR merge metrics
- No merged PRs in 30d
Description
Hi, you may wish to increase the default number of iterations in fastpca (fastiter), for some datasets the default is too low, resulting in inaccurate estimation of eigenvectors (I checked this by comparing the non-fastmode results with the fastmode, and verified with several other SVD implementations).
For example with the default iterations:
> diag(cor(P1, P2))
V2 V3 V4 V5 V6 V7 V8
0.9985658 0.9909673 0.9819172 -0.9131868 0.9447627 0.9555776 -0.8435918
V9 V10 V11
-0.7538453 -0.6555316 0.8961565
With fastiter: 100
> diag(cor(P1, P2))
V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
1 1 1 -1 -1 -1 -1 1 1 1
where P1 and P2 are the top ten eigenvectors from non-fastmode and fastmode, respectively. The dataset consists of 5300 individuals with 3700 LD-thinned SNPs.
I'm using v6.1.1.
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the fastpca fastmode implementation and the fastiter default. Compare fastmode eigenvectors with non-fastmode results on the reported dataset, including fastiter 100; done when the default produces accurate results comparable to the non-fastmode and other SVD implementations.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- c
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100