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bedrock.bio

open_targets.credible_set

import bedrock_bio as bb

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

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
studyLocusId studyId variantId chromosome position region beta zScore pValueMantissa pValueExponent ... purityMinR2 locusStart locusEnd sampleSize ldSet locus confidence studyType isTransQtl version
0 04af2405ad26242e70bd071d5bf6cc66 gtex-v10_majiq_blood_ensg00000250575_s_492350-... 1_17005_A_G 1 17005 chr1:-506759-1493241 1.003750 NaN 1.559 -7 ... NaN <NA> <NA> <NA> <NA> [{'is95CredibleSet': True, 'is99CredibleSet': ... SuSiE fine-mapped credible set with in-sample LD sqtl False 26.09
1 fc9d58f49fd994b04f3a422d533b5519 gtex-v10_majiq_spleen_ensg00000227232_s_17526-... 1_17005_A_G 1 17005 chr1:-970430-1029570 1.214680 NaN 4.937 -6 ... NaN <NA> <NA> <NA> <NA> [{'is95CredibleSet': True, 'is99CredibleSet': ... SuSiE fine-mapped credible set with in-sample LD sqtl False 26.09
2 35c4c4d4194889bb1f6ccb3585674a12 gtex-v10_majiq_lung_ensg00000279457_t_185217-1... 1_17005_A_G 1 17005 chr1:-804589-1195411 -0.917062 NaN 1.286 -6 ... NaN <NA> <NA> <NA> <NA> [{'is95CredibleSet': True, 'is99CredibleSet': ... SuSiE fine-mapped credible set with in-sample LD sqtl False 26.09
3 05f9696bf4ddaef3f848f73dd20763f1 gtex-v10_majiq_pancreas_ensg00000279457_t_1852... 1_17005_A_G 1 17005 chr1:-804589-1195411 1.237840 NaN 2.573 -7 ... NaN <NA> <NA> <NA> <NA> [{'is95CredibleSet': True, 'is99CredibleSet': ... SuSiE fine-mapped credible set with in-sample LD sqtl False 26.09
4 b601b39829682421fb99cfb78485ffb4 GCST90474483 1_51427_T_G 1 51427 NaN -0.437719 NaN 1.275 -10 ... NaN <NA> <NA> 8282 [{'tagVariantId': '1_51427_T_G', 'r2Overall': ... [{'is95CredibleSet': True, 'is99CredibleSet': ... PICS fine-mapped credible set extracted from s... gwas <NA> 26.09

Description

Section titled “Description”

95% credible sets for GWAS and molQTL studies.

Credible sets include all variants in the credible set as well as the fine-mapping method and statistics used to estimate the credible set [Genetics]

Partitions

Section titled “Partitions”

Not partitioned.

Schema

Section titled “Schema”
Column Type Description
studyLocusId TEXT Study-locus identifier for the credible set
studyId TEXT Identifier for the study which the credible set is derived
variantId TEXT The lead variant for the credible set, by posterior probability
chromosome TEXT Chromosome which the credible set is located
position INT Position of the lead variant for the credible set (GRCh38)
region TEXT Start and end positions of the region used for fine-mapping
beta DOUBLE Beta coefficient of the lead variant
zScore DOUBLE Z-score of the lead variant from the GWAS
pValueMantissa FLOAT Mantissa value of the lead variant P-value
pValueExponent INT Exponent value of the lead variant P-value
effectAlleleFrequencyFromSource FLOAT Allele frequency of the lead variant from the GWAS
standardError DOUBLE Standard error of the lead variant
subStudyDescription TEXT [Deprecated]
qualityControls TEXT[] Quality control flags for this credible set
finemappingMethod TEXT Method used for fine-mapping of credible set
credibleSetIndex INT Integer label for the order of credible sets from study-region
credibleSetlog10BF DOUBLE Log10 Bayes factor for the entire credible set
purityMeanR2 DOUBLE Mean R-squared linkage disequilibrium for variants in the credible set
purityMinR2 DOUBLE Minimum R-squared linkage disequilibrium for variants in the credible set
locusStart INT Start position of the region that was fine-mapped for this credible set
locusEnd INT End position of the region that was fine-mapped for this credible set
sampleSize INT Sample size of the study from which this credible set is derived
ldSet STRUCT(tagVariantId TEXT, r2Overall DOUBLE)[] Array of structs which denote the variants in LD with the credible set lead variant
locus STRUCT(is95CredibleSet BOOLEAN, is99CredibleSet BOOLEAN, logBF DOUBLE, posteriorProbability DOUBLE, variantId TEXT, pValueMantissa FLOAT, pValueExponent INT, beta DOUBLE, standardError DOUBLE, r2Overall DOUBLE)[] Array of structs which denote the variants within the credible set
confidence TEXT Description of how this credible set was derived in terms of data and fine-mapping method
studyType TEXT Descriptor for whether the credible set is derived from GWAS or molecular QTL
isTransQtl BOOLEAN Boolean for whether this credible set is a trans-pQTL or not
version TEXT Open Targets Platform release version (major.minor), e.g. 26.09. Added during ingest.