Hello,
I was wondering where i can find the json files of the colocalisation analysis of OT genetics.
Thank you in advance
Hello,
I was wondering where i can find the json files of the colocalisation analysis of OT genetics.
Thank you in advance
Hi,
The colocalization datasets can be downloaded from here: ftp://ftp.ebi.ac.uk/pub/databases/opentargets/genetics/latest/v2d_coloc
in parquet format.
The schema of the dataset looks like this:
root
|-- coloc_n_vars: integer (nullable = true)
|-- coloc_h0: double (nullable = true)
|-- coloc_h1: double (nullable = true)
|-- coloc_h2: double (nullable = true)
|-- coloc_h3: double (nullable = true)
|-- coloc_h4: double (nullable = true)
|-- left_type: string (nullable = true)
|-- left_study: string (nullable = true)
|-- left_chrom: string (nullable = true)
|-- left_pos: integer (nullable = true)
|-- left_ref: string (nullable = true)
|-- left_alt: string (nullable = true)
|-- right_type: string (nullable = true)
|-- right_study: string (nullable = true)
|-- right_bio_feature: string (nullable = true)
|-- right_phenotype: string (nullable = true)
|-- right_chrom: string (nullable = true)
|-- right_pos: integer (nullable = true)
|-- right_ref: string (nullable = true)
|-- right_alt: string (nullable = true)
|-- coloc_h4_h3: double (nullable = true)
|-- coloc_log2_h4_h3: double (nullable = true)
|-- is_flipped: boolean (nullable = true)
|-- right_gene_id: string (nullable = true)
|-- left_var_right_study_beta: double (nullable = true)
|-- left_var_right_study_se: double (nullable = true)
|-- left_var_right_study_pval: double (nullable = true)
|-- left_var_right_isCC: boolean (nullable = true)
As the dataset is specific for colocalization, you might need to join the table with association and study level information stored under https://ftp.ebi.ac.uk/pub/databases/opentargets/genetics/latest/v2d/
.
Please let us know if thereβs anything else we can help with!
Best,
Daniel