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Create an LD loader for on-demand block-wise LD retrieval

Source: R/ld_loader.R
ld_loader.Rd

Constructs a loader function that retrieves per-block LD matrices on demand. This avoids loading all blocks into memory simultaneously, which is critical for genome-wide analyses with hundreds of blocks.

Usage

ld_loader(
  R_list = NULL,
  X_list = NULL,
  ld_meta_path = NULL,
  regions = NULL,
  LD_info = NULL,
  return_genotype = FALSE,
  max_variants = NULL
)

Arguments

R_list

List of G precomputed LD correlation matrices (p_g x p_g).

X_list

List of G genotype matrices (n x p_g).

ld_meta_path

Path to a pecotmr LD metadata TSV file (as used by load_LD_matrix).

regions

Character vector of G region strings (e.g., "chr22:17238266-19744294"). Required when ld_meta_path is used.

LD_info

A data.frame with column LD_file (paths to genotype files or .cor.xz LD matrix files) and optionally SNP_file (paths to companion .bim files for pre-computed blocks; defaults to paste0(LD_file, ".bim") if absent). Genotype paths can be PLINK2 prefixes, PLINK1 prefixes, VCF files, or GDS files. As returned by cTWAS meta-data utilities.

return_genotype

Logical. When using region mode, return the genotype matrix X (TRUE) or LD correlation R (FALSE, default).

max_variants

Integer or NULL. If set, randomly subsample blocks larger than this to control memory usage.

Value

A function loader(g) that, given a block index g, returns the corresponding LD matrix or genotype matrix.

Details

Four modes are supported:

list mode (R)

Pre-loaded list of LD correlation matrices. Simple but uses more memory. Set R_list.

list mode (X)

Pre-loaded list of genotype matrices (n x p_g). Set X_list.

region mode

Loads LD from a pecotmr metadata TSV file on the fly via load_LD_matrix. Memory-efficient for large datasets. Set ld_meta_path and regions.

LD_info mode

Loads pre-computed LD blocks from .cor.xz files listed in an LD_info data.frame (as returned by cTWAS meta-data utilities). Set LD_info.

Examples

# List mode with pre-computed LD
R1 <- diag(10)
R2 <- diag(15)
loader <- ld_loader(R_list = list(R1, R2))
loader(1)  # returns R1
#>       [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#>  [1,]    1    0    0    0    0    0    0    0    0     0
#>  [2,]    0    1    0    0    0    0    0    0    0     0
#>  [3,]    0    0    1    0    0    0    0    0    0     0
#>  [4,]    0    0    0    1    0    0    0    0    0     0
#>  [5,]    0    0    0    0    1    0    0    0    0     0
#>  [6,]    0    0    0    0    0    1    0    0    0     0
#>  [7,]    0    0    0    0    0    0    1    0    0     0
#>  [8,]    0    0    0    0    0    0    0    1    0     0
#>  [9,]    0    0    0    0    0    0    0    0    1     0
#> [10,]    0    0    0    0    0    0    0    0    0     1
loader(2)  # returns R2
#>       [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
#>  [1,]    1    0    0    0    0    0    0    0    0     0     0     0     0
#>  [2,]    0    1    0    0    0    0    0    0    0     0     0     0     0
#>  [3,]    0    0    1    0    0    0    0    0    0     0     0     0     0
#>  [4,]    0    0    0    1    0    0    0    0    0     0     0     0     0
#>  [5,]    0    0    0    0    1    0    0    0    0     0     0     0     0
#>  [6,]    0    0    0    0    0    1    0    0    0     0     0     0     0
#>  [7,]    0    0    0    0    0    0    1    0    0     0     0     0     0
#>  [8,]    0    0    0    0    0    0    0    1    0     0     0     0     0
#>  [9,]    0    0    0    0    0    0    0    0    1     0     0     0     0
#> [10,]    0    0    0    0    0    0    0    0    0     1     0     0     0
#> [11,]    0    0    0    0    0    0    0    0    0     0     1     0     0
#> [12,]    0    0    0    0    0    0    0    0    0     0     0     1     0
#> [13,]    0    0    0    0    0    0    0    0    0     0     0     0     1
#> [14,]    0    0    0    0    0    0    0    0    0     0     0     0     0
#> [15,]    0    0    0    0    0    0    0    0    0     0     0     0     0
#>       [,14] [,15]
#>  [1,]     0     0
#>  [2,]     0     0
#>  [3,]     0     0
#>  [4,]     0     0
#>  [5,]     0     0
#>  [6,]     0     0
#>  [7,]     0     0
#>  [8,]     0     0
#>  [9,]     0     0
#> [10,]     0     0
#> [11,]     0     0
#> [12,]     0     0
#> [13,]     0     0
#> [14,]     1     0
#> [15,]     0     1