Comments (4)
Thank you for your gracious and patient response.
Best regards,
Yuran
from tensorqtl.
Yes that's expected — to avoid artifacts due to outlier effects, a MAF filter that depends on the interaction term is applied (i.e., variants with MAF ≥ 0.05 in the samples belonging to each of the top and bottom halves of the interaction term). This can be adjusted with --maf_threshold_interaction
. Please see section "Identification of cell type interaction eQTLs and sQTLs" in the supplement of https://www.science.org/doi/10.1126/science.aaz8528 for additional details.
from tensorqtl.
Thank you for your reply. Under the same phenotype and genotype background, changing only the cell score covariate of the interaction term can also lead to differences in the overall SNP gene pair of the test.
Can I understand that when testing each gene, only variations belonging to the upper and lower parts of the cell score distribution were considered, and the frequency of secondary alleles for these variations was not less than 5%?
This phenomenon is not caused by operational errors.
from tensorqtl.
That's almost right. It's the samples that were split into those belonging to the upper and lower parts of the cell score distribution, and MAF was computed separately for each of those two groups. Only variants that passed the MAF filter in both groups were retained. If you want to avoid this, you can set --maf_threshold_interaction 0
,
from tensorqtl.
Related Issues (20)
- missing tss_distance in cis output HOT 1
- scipy.optimize.newton failed to converge HOT 1
- Warning and Error in tensorQTL trans mode HOT 9
- Memory Allocation Issue during trans-QTL Mapping HOT 3
- Issues with TensorQTL in Trans Mode
- AttributeError: 'dict' object has no attribute 'T' tensorqtl HOT 2
- broken link HOT 1
- Tensorqtl installation HOT 3
- No credible sets output from susie.map because pval_nominal=0 HOT 2
- ValueError: array must not contain infs or NaNs
- interaction HOT 1
- [Susie] ValueError: prior variance must be non-negative HOT 4
- [trans] trans.map_permutations(): KeyError: 'r2' HOT 2
- [map_trans] R2 not returned in interaction analysis HOT 2
- [pval post-processing] Interaction output for cis/trans
- Which beta coresponds to which allele in the outputs?
- cis-mapping with interaction
- Errors in the BackgroundGenerator cause main thread to get stuck
- Questions about the `map_permutations` and `apply_permutations` functions
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from tensorqtl.