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Retrieve GWAS credible set data

Source: R/gwasCredibleSet.R
gwasCredibleSet.Rd

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 (e.g GCST90002357).

variant_id

Character: generated ID for variants by Open Targets (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

if (FALSE) { # \dontrun{
result <- gwasCredibleSet(study_id="GCST90002357", 
variant_id="1_154119580_C_A")
result <- gwasCredibleSet(study_id="GCST90002357", variant_id="rs2494663")
} # }