Retrieve calculated QTL summary statistics for credible variant set.
Source:R/qtlCredibleSet.R
qtlCredibleSet.Rd
In Open Targets Genetics, the lead variants are expanded into a more comprehensive set of candidate causal variants referred to as the tag variants. This function retrieves calculated summary statistics for tag variants included in a lead variant colocalization analysis for a given study (which links a top loci with a trait). The user can filter the results by desired biofeature (e.g tissue, cell type,...) the function obtains tag variant information.
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).
- gene
Character: Gene ENSEMBL ID (e.g. ENSG00000169174) or gene symbol (e.g. PCSK9).
- biofeature
Character: Represents either a tissue, cell type, aggregation type, protein type, etc.
Value
Returns a data frame of results from the QTL credible set of variants consisting of the following columns:
tagVariant.id
: Character vector. Tag variant ID.tagVariant.rsId
: Character vector. Tag variant rsID.pval
: Numeric. P-value.se
: Numeric. Standard error.beta
: Numeric. Beta value.postProb
: Numeric. Posterior probability.MultisignalMethod
: Character vector. Multisignal method.logABF
: Numeric. Logarithm of approximate Bayes factor.is95
: Logical. Indicates if the variant has a 95is99
: Logical. Indicates if the variant has a 99