Get LD Correlation Matrix

Extract the LD correlation matrix from an LdData object. If only a genotype handle is available, recomputes R from genotypes on the fly.

Usage

getCorrelation(x)

# S4 method for class 'LdData'
getCorrelation(x)

Arguments

x

An LdData object.

Value

A correlation matrix, or a list of per-block matrices.

Examples

data(eqtlRegionExample)
X <- eqtlRegionExample$X[, 1:8]
gr <- GenomicRanges::GRanges("22",
  IRanges::IRanges(seq(1L, by = 100L, length.out = 8), width = 1L))
ld <- LdData(correlation = cor(X), variants = gr,
  blockMetadata = S4Vectors::DataFrame(
    chrom = "22", start = 1L, end = 1000L))
getCorrelation(ld)
#>                    chr22:32119788:T:C chr22:32119867:T:G chr22:32119961:T:G
#> chr22:32119788:T:C         1.00000000         1.00000000         -0.3896071
#> chr22:32119867:T:G         1.00000000         1.00000000         -0.3896071
#> chr22:32119961:T:G        -0.38960714        -0.38960714          1.0000000
#> chr22:32120053:T:C        -0.07607973        -0.07607973         -0.1431621
#> chr22:32120593:A:G        -0.07607973        -0.07607973         -0.1431621
#> chr22:32120636:T:C        -0.16985384        -0.16985384         -0.2327461
#> chr22:32120932:G:A         0.64492502         0.64492502         -0.2595210
#> chr22:32120975:A:G        -0.11897144        -0.11897144         -0.1416922
#>                    chr22:32120053:T:C chr22:32120593:A:G chr22:32120636:T:C
#> chr22:32119788:T:C        -0.07607973        -0.07607973        -0.16985384
#> chr22:32119867:T:G        -0.07607973        -0.07607973        -0.16985384
#> chr22:32119961:T:G        -0.14316214        -0.14316214        -0.23274610
#> chr22:32120053:T:C         1.00000000         1.00000000        -0.09691283
#> chr22:32120593:A:G         1.00000000         1.00000000        -0.09691283
#> chr22:32120636:T:C        -0.09691283        -0.09691283         1.00000000
#> chr22:32120932:G:A        -0.01898060        -0.01898060        -0.14868888
#> chr22:32120975:A:G        -0.08068061        -0.08068061         0.68622457
#>                    chr22:32120932:G:A chr22:32120975:A:G
#> chr22:32119788:T:C          0.6449250        -0.11897144
#> chr22:32119867:T:G          0.6449250        -0.11897144
#> chr22:32119961:T:G         -0.2595210        -0.14169222
#> chr22:32120053:T:C         -0.0189806        -0.08068061
#> chr22:32120593:A:G         -0.0189806        -0.08068061
#> chr22:32120636:T:C         -0.1486889         0.68622457
#> chr22:32120932:G:A          1.0000000        -0.12097213
#> chr22:32120975:A:G         -0.1209721         1.00000000