Ignoring individuals in EIGENSOFT in IND file
Nobody has claimed this yet.
- Dominant language
- C
- Stars
- 207
- Forks
- 61
- PR merge metrics
- No merged PRs in 30d
Description
Dear All,
I am trying to run Eigensoft's SMARTPCA module for my PCA analysis on world-wide populations of 1000 G together with my own samples. However, when i run SMARTPCA with remove outlier options, it removes some samples from 1000G populations and from my data set.
So, I run the SMARTPCA again (without outlier removal option) while ignoring the some of the outlier individuals in the "*.ind" file. as:
HG04239 M SAS
NA06984 M ???
NA06985 F ???
NA06986 M ???
NA10847 F CEU
NA10851 M CEU
NA11829 M CEU
NA11830 F CEU
But the E-values still calculated in the resultant output files for the individuals marked. Can anyone kindly guide me how to format the "ind" file to ignore some individuals from subset of populations?
Thank you very much!
--sohail
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 checking SMARTPCA's handling of the *.ind file and its outlier or ignore settings; the issue provides no repository file or test to target. Done means documenting the valid syntax for excluding individuals and explaining whether excluded samples should still receive E-values.
Written by the indexing model from the issue text.
Assessment
- Domain
- tooling
- Issue type
- Documentation
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100