Compute Between-Credible-Set Correlation On Demand

Compute the between-credible-set correlation matrix for a fineMappingRow on demand from an LD source. The correlation is a view over the fit-time LD, which lives on the data object — a QtlDataset's genotypes or a QtlSumStats / GwasSumStats LD sketch — and is deliberately never stored on the fit. An ldSource is therefore always required.

Usage

computeCsCorrelation(x, ldSource, ...)

# S4 method for class 'FineMappingResultBase,SumStatsBase'
computeCsCorrelation(x, ldSource, ...)

# S4 method for class 'FineMappingResultBase,QtlDataset'
computeCsCorrelation(x, ldSource, ...)

# S4 method for class 'FineMappingResultBase,ANY'
computeCsCorrelation(x, ldSource, ...)

Arguments

x

A fineMappingRow carrying the fit (credible-set membership and PIP) and its variant ids.

ldSource

The object supplying the LD: a QtlDataset (individual-level; genotypes via getGenotypes) or a QtlSumStats / GwasSumStats (summary statistics; LD via getLdSketch). Any other type is an error.

...

Passed to methods.

Value

A numeric m x m between-credible-set correlation matrix (m = number of credible sets), or NULL when the fit has fewer than two credible sets.

Examples

data(qtlFineMappingPairedExample)
data(qtlSumStatsExample)
fe <- getFineMappingResult(qtlFineMappingPairedExample)
computeCsCorrelation(fe, qtlSumStatsExample)
#>             L2          L3
#> L2  1.00000000 -0.08404977
#> L3 -0.08404977  1.00000000