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bedrock.bio

open_targets.colocalisation

import bedrock_bio as bb

rel = bb.load_table('open_targets.colocalisation')

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
Sample output (5 rows, showing 8 of 11 columns)
   leftStudyLocusId         | rightStudyLocusId        | rightStudyType | chromosome | colocalisationMethod | numberColocalisingVariants | h3                  | h4
   ------------------------ | ------------------------ | -------------- | ---------- | -------------------- | -------------------------- | ------------------- | ------------------
0  417a583041057b8442473b3… | 04e75ceefda5da8dab91a14… | gwas           | 1          | COLOC_PIP_ECAVIAR    | 101                        | 0.15438633055829845 | 0.8456136694417016
1  524f9abb6294b0b37c24261… | 08a2af0c0290dc89796839f… | gwas           | 1          | COLOC_PIP_ECAVIAR    | 90                         | 0.09053841019556734 | 0.9094615898044326
2  6b9bf3f8928cf7715967ca6… | 190e474125af8cfc33d4e61… | gwas           | 1          | COLOC_PIP_ECAVIAR    | 88                         | 0.21789427692494218 | 0.7821057230750579
3  3d38145b5224c566fab0aef… | 2f3a76bcaae0200213eb814… | gwas           | 1          | COLOC_PIP_ECAVIAR    | 167                        | 0.2089134404526324  | 0.7910865595473676
4  1750046c03e32f280049626… | 2ee885bd2aead0353f3f8f5… | tuqtl          | 1          | COLOC_PIP_ECAVIAR    | 5                          | 0.2051889692287292  | 0.7948110307712708

Description

Section titled “Description”

GWAS-GWAS and GWAS-molQTL credible set colocalisation results using colocPIP and eCAVIAR methods.

Dataset includes colocalising pairs and the statistics used to estimate the colocalisation [Genetics]

Partitions

Section titled “Partitions”

Not partitioned.

Schema

Section titled “Schema”
Column Type Description
leftStudyLocusId TEXT Study-locus identifier for left-side overlapping signal
rightStudyLocusId TEXT Study-locus identifier for right-side overlapping signal
rightStudyType TEXT Type of the right-side study (e.g., gwas, eqtl)
chromosome TEXT Chromosome where the colocalisation occurs
colocalisationMethod TEXT Method used to estimate colocalisation (e.g., coloc)
numberColocalisingVariants BIGINT Number of variants intersecting between two overlapping study-loci
h3 DOUBLE Posterior probability that both traits are associated, but with different causal variants (H3)
h4 DOUBLE Posterior probability that both traits are associated and share a causal variant (H4)
clpp DOUBLE Colocalisation posterior probability (CLPP) score estimating the probability of shared causal variants
betaRatioSignAverage DOUBLE Average sign of the beta ratio between colocalised variants
version TEXT Open Targets Platform release version (major.minor), e.g. 26.09. Added during ingest.