snp_ld_scores: LD scores

In bigsnpr: Analysis of Massive SNP Arrays

LD scores

Description

LD scores

Usage

snp_ld_scores(
  Gna,
  ind.row = rows_along(Gna),
  ind.col = cols_along(Gna),
  size = 500,
  infos.pos = NULL,
  ncores = 1
)

bed_ld_scores(
  obj.bed,
  ind.row = rows_along(obj.bed),
  ind.col = cols_along(obj.bed),
  size = 500,
  infos.pos = NULL,
  ncores = 1
)

Arguments

Gna	A FBM.code256 (typically ⁠<bigSNP>$genotypes⁠). You can have missing values in these data.
ind.row	An optional vector of the row indices (individuals) that are used. If not specified, all rows are used. Don't use negative indices.
ind.col	An optional vector of the column indices (SNPs) that are used. If not specified, all columns are used. Don't use negative indices.
size	For one SNP, window size around this SNP to compute correlations. Default is 500. If not providing infos.pos (NULL, the default), this is a window in number of SNPs, otherwise it is a window in kb (genetic distance).
infos.pos	Vector of integers specifying the physical position on a chromosome (in base pairs) of each SNP. Typically ⁠<bigSNP>$map$physical.pos⁠.
ncores	Number of cores used. Default doesn't use parallelism. You may use bigstatsr::nb_cores().
obj.bed	Object of type bed, which is the mapping of some bed file. Use obj.bed <- bed(bedfile) to get this object.

Value

A vector of LD scores. For each variant, this is the sum of squared correlations with the neighboring variants (including itself).

Examples

test <- snp_attachExtdata()
G <- test$genotypes

(ld <- snp_ld_scores(G, ind.col = 1:1000))

bigsnpr documentation built on Sept. 30, 2024, 9:18 a.m.