Compute Block LD Correlation

Compute the LD correlation matrix for a block of SNPs. Delegates to computeLd for the actual computation, with automatic backend selection based on file format unless overridden.

Usage

computeBlockLdCor(handle, snpIdx, backend = "internal", method = "sample", ...)

Arguments

handle

A GenotypeHandle object.

snpIdx

Integer vector of 1-based SNP indices.

backend

Character, one of "internal" (default), "snprelate", or "snpstats". When "internal", GDS-format handles automatically use SNPRelate::snpgdsLDMat via the native GDS path; other formats use the internal correlator.

method

Character, LD computation method passed to computeLd. Default "sample".

...

Additional arguments passed to computeLd (e.g., shrinkage, trimSamples).

Value

Numeric correlation matrix (p x p).