Get LD Reference

Return the LD reference of this object: a genotype panel (see readGenotypes), a GenotypeMixture or an LdMatrix. Defined on classes that embed an ldReference slot: GwasSumStats, QtlSumStats, FineMappingResultBase, TwasWeights, ColocResultBase and LdStatistic, whose reference is the panel it reads its blocks' LD from. Returns NULL when the slot is unset (e.g. a TwasWeights fit from individual-level data via QtlDataset, or an LdStatistic built from LdMatrix blocks).

Usage

ldReference(x, ...)

# S4 method for class 'SumStatsBase'
ldReference(x)

# S4 method for class 'FineMappingResultBase'
ldReference(x)

# S4 method for class 'ColocResultBase'
ldReference(x)

# S4 method for class 'LdStatistic'
ldReference(x)

# S4 method for class 'TwasWeights'
ldReference(x)

Arguments

x

An S4 object that carries an ldReference slot.

...

Unused.

Value

A RangedSummarizedExperiment genotype panel, a GenotypeMixture, an LdMatrix, or NULL.

Examples

data(qtlSumStatsExample)
ldReference(qtlSumStatsExample)
#> class: RangedSummarizedExperiment 
#> dim: 200 165 
#> metadata(1): genotypeSource
#> 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):