gwasCredibleSet: Retrieve GWAS credible set data

In otargen: Access Open Target Genetics

Retrieve GWAS credible set data

Description

Provided with a study ID and a lead variant ID, this function returns a data frame consisting of all the associated credible set tag variants with the corresponding statistical data.

Usage

gwasCredibleSet(study_id, variant_id)

Arguments

study_id	Character: Study ID(s) generated by Open Targets Genetics (e.g GCST90002357).
variant_id	Character: generated ID for variants by Open Targets Genetics (e.g. 1_154119580_C_A) or rsId (rs2494663).

Value

Returns a data frame of results from the credible set of variants for a specific lead variant with the following columns:

• tagVariant.id: Data frame. A table of IDs of the tag variant.

• tagVariant.rsId: Character vector. rsID of the tag variant.

• beta: Numeric. Beta value.

• postProb: Numeric. Posterior probability.

• pval: Numeric. P-value.

• se: Numeric. Standard error.

• MultisignalMethod: Character vector. Multisignal method.

• logABF: Numeric. Logarithm of approximate Bayes factor.

• is95: Logical. Indicates if the variant has a 95

• is99: Logical. Indicates if the variant has a 99

Examples

## Not run: 
result <- gwasCredibleSet(study_id="GCST90002357", variant_id="1_154119580_C_A")
result <- gwasCredibleSet(study_id="GCST90002357", variant_id="rs2494663")

## End(Not run)

otargen documentation built on Sept. 30, 2024, 9:43 a.m.