Get Per-Row Trait Positions

Return the molecular feature's OWN genomic coordinates (the gene / peak range; TSS = start()) for each row of a per-tuple collection, as a GRanges with one range per row. Distinct from getRegion (the fine-mapping window for a FineMappingResult): the true trait position cannot be inferred from summary statistics, so it is threaded from the QtlDataset rowRanges or an explicit QtlSumStats trait-position and carried as provenance onto QtlFineMappingResult and TwasWeights.

Usage

getTraitPosition(x, ...)

# S4 method for class 'FineMappingResultBase'
getTraitPosition(x, ...)

# S4 method for class 'QtlDataset'
getTraitPosition(x, traitId = NULL, ...)

# S4 method for class 'QtlSumStats'
getTraitPosition(x, traitId = NULL, ...)

# S4 method for class 'TwasWeights'
getTraitPosition(x, ...)

Arguments

x

The object.

...

Reserved for future use.

traitId

Character or NULL. Molecular trait / feature identifier to select; NULL matches all traits in the dataset.

Value

A GRanges with one range per row of x, or an empty GRanges when the collection carries no trait-position provenance.

Examples

data(qtlDatasetExample)
getTraitPosition(qtlDatasetExample)
#> GRanges object with 1 range and 0 metadata columns:
#>                seqnames            ranges strand
#>                   <Rle>         <IRanges>  <Rle>
#>   ENSG_example    chr22 15680768-15681267      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths