Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Ensure joins between annotation and scores metadata are always unique. #8

Open
whimsial opened this issue Mar 6, 2023 · 0 comments
Assignees
Labels
enhancement New feature or request

Comments

@whimsial
Copy link
Member

whimsial commented Mar 6, 2023

The current code is not future proof because new labelling scheme for the genome-wide trans scores allows for duplicated scoreids. In fact, we store as many duplicated scoreids as there are individual scores contributing to each genome-wide trans score. Therefore, joins with annotation tables may fail.

To address this we need to extend the original key to also include locus start and end position by changing these (and similar) lines:

setkey(transqtl.loci, scoreid)
setkey(trans.genome.wide.scoresinfo, scoreid)

to:

setkey(transqtl.loci, scoreid, x.startpos, x.endpos)
setkey(trans.genome.wide.scoresinfo, scoreid, x.startpos, x.endpos)

@dlipschu, we need to check that this change does not affect your results.

@whimsial whimsial added the enhancement New feature or request label Mar 6, 2023
@whimsial whimsial self-assigned this Mar 6, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

No branches or pull requests

1 participant