Comments (2)
Thanks! I'll try it out, but I think this will be random enough for my purposes.
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This is a good point, and indeed how ties are assigned by default. I added an option to randomly select the top variant in case of ties (45353a8). This is enabled with cis.map_cis(..., random_tiebreak=True)
. In some cases, the comparison to the maximum value doesn't select all possible ties due to machine epsilon. If this is an issue I can add some tolerance with isclose
.
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Related Issues (20)
- Expected format for --interaction parameter HOT 2
- How to use Plink2 files including multiallelic file HOT 2
- An error in tensorqtl_examples.ipynb ? HOT 1
- Reproduce GTEx v8 HOT 3
- Interaction mode: k variable overwrite in cis.py script (v1.0.7) HOT 1
- nominal p value threshold for non-top eVariants in interaction mode
- missing pval_nominal_threshold column in output cis_qtl.txt file HOT 1
- Output Documentation HOT 3
- TensorQTL load Plink2 files in command line HOT 1
- Can we use tensorqtl without a covariate? HOT 1
- Cannot run cis.map_independent HOT 4
- TypeError of interaction mode when removing the command "--best-only" HOT 1
- problematic variant HOT 1
- NaN values in some mQTLs parquet file HOT 5
- Allele frequency reported in nominal cis-mQTLs output HOT 1
- TensorQTL for non-genomic data HOT 4
- Regression with phenotype containing 4 expressed genes HOT 1
- Limit the number of multi-threading HOT 1
- Question - genetic data from related HOT 1
- --paired_covariate support for cis_nominal HOT 2
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