Skip to contents

Genome-Wide LD Block Detection by Chromosome

Source: R/run_and_tune.R
run_Big_LD_all_chr.Rd

Applies Big_LD() chromosome by chromosome, collects results and returns a single tidy data frame annotated with chromosome and block length. This is the recommended entry point for genome-wide analyses.

Usage

run_Big_LD_all_chr(
  geno_matrix,
  snp_info = NULL,
  CLQcut = 0.5,
  method = c("r2", "rV2"),
  n_threads = 1L,
  clstgap = 40000,
  leng = 200,
  subSegmSize = 1500,
  MAFcut = 0.05,
  appendrare = FALSE,
  singleton_as_block = FALSE,
  checkLargest = FALSE,
  CLQmode = "Density",
  kin_method = "chol",
  split = FALSE,
  digits = -1L,
  seed = NULL,
  min_snps_chr = 10L,
  chr = NULL,
  clean_malformed = FALSE,
  max_bp_distance = 0L,
  verbose = FALSE
)

Arguments

geno_matrix

Numeric matrix (individuals x SNPs; values 0/1/2), spanning all chromosomes.

snp_info

Data frame with columns CHR, SNP, POS. Column order is flexible; columns are matched by name.

CLQcut, clstgap, leng, subSegmSize, MAFcut, appendrare, checkLargest, CLQmode, kin_method, split, digits, seed, verbose

Forwarded to Big_LD(). See that function's documentation for details.

method

Character. LD metric: "r2" (default, standard squared Pearson correlation) or "rV2" (kinship-adjusted). See Big_LD() for details.

n_threads

Integer. Number of OpenMP threads for the C++ LD kernel. Default 1L. Increase for multi-core systems.

singleton_as_block

Logical. If TRUE, SNPs that pass MAF filtering but are not assigned to any clique are returned as single-SNP blocks (start == end, length_bp == 1). Default FALSE. See Big_LD() for details.

min_snps_chr

Integer. Chromosomes with fewer SNPs than this after MAF filtering are skipped. Default 10L. Increase to skip small scaffolds in whole-genome datasets.

chr

Character vector or NULL. If supplied, only the named chromosomes are processed. Labels must match the values in snp_info$CHR after normalisation (no chr prefix). E.g. chr = c("1","3","5") or chr = "X". Default NULL processes all chromosomes.

clean_malformed

Logical. If TRUE, stream-clean the input file before reading by removing lines whose column count does not match the header. Only relevant when geno_matrix is a file path wrapped into a backend. Default FALSE.

max_bp_distance

Integer. Maximum base-pair distance between a SNP pair for its r\(^2\) to be computed. Pairs beyond this distance are set to zero in the adjacency matrix (assumed to be in negligible LD). 0L (default) disables this and computes all pairs (original behaviour). Recommended value for WGS panels: 500000L (500 kb). Has no effect when CLQmode is "Louvain" or "Leiden" and the window spans less than max_bp_distance. Requires sorted SNP positions within each sub-segment (guaranteed by run_Big_LD_all_chr).

Value

A data.frame with columns: start, end, start.rsID, end.rsID, start.bp, end.bp, CHR, length_bp. Rows are sorted by CHR then start.bp.

See also

Big_LD(), tune_LD_params, extract_haplotypes

Examples

# \donttest{
# Use the package example data -- 120 individuals, 230 SNPs, 3 chromosomes,
# 9 simulated LD blocks (3 per chromosome).
data(ldx_geno,     package = "LDxBlocks")
data(ldx_snp_info, package = "LDxBlocks")
blocks <- run_Big_LD_all_chr(
  ldx_geno, ldx_snp_info,
  method = "r2", CLQcut = 0.55, leng = 15L,
  subSegmSize = 100L, verbose = FALSE
)
head(blocks)
#>   start end start.rsID end.rsID start.bp end.bp n_snps CHR length_bp
#> 1     1  25     rs1001   rs1025     1000  25027     25   1     24028
#> 2    31  50     rs1031   rs1050    81064  99022     20   1     17959
#> 3    56  80     rs1056   rs1080   155368 179371     25   1     24004
#> 4     1  30     rs2001   rs2030     1000  30023     30   2     29024
#> 5    36  55     rs2036   rs2055    86236 105290     20   2     19055
#> 6    61  80     rs2061   rs2080   161515 180473     20   2     18959
summarise_blocks(blocks)
#>      CHR n_blocks min_bp median_bp  mean_bp max_bp total_bp_covered
#> 1      1        3  17959     24004 21997.00  24028            65991
#> 2      2        3  18959     19055 22346.00  29024            67038
#> 3      3        3  18069     18356 18385.00  18730            55155
#> 4 GENOME        9  17959     18959 20909.33  29024           188184
# }