Get LD Sketch

Return the genotype panel carrying the LD reference for this collection. Defined on classes that embed an ldSketch slot: GwasSumStats, QtlSumStats, FineMappingResult, TwasWeights. Returns NULL when the slot is unset (e.g. a TwasWeights fit from individual-level data via QtlDataset).

Usage

getLdSketch(x, ...)

# S4 method for class 'SumStatsBase'
getLdSketch(x, ...)

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

# S4 method for class 'ColocResultBase'
getLdSketch(x, ...)

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

Arguments

x

An S4 object that carries an ldSketch slot.

...

Unused.

Value

A RangedSummarizedExperiment genotype panel, or NULL.

Examples

data(qtlSumStatsExample)
getLdSketch(qtlSumStatsExample)
#> class: RangedSummarizedExperiment 
#> dim: 200 165 
#> metadata(0):
#> assays(1): dosage
#> rownames(200): chr22:14560203:A:G chr22:14564328:T:C ...
#>   chr22:15826914:T:G chr22:15826991:T:C
#> rowData names(3): SNP A1 A2
#> colnames(165): NA06989 NA11891 ... NA10854 NA12865
#> colData names(0):