loci_ld_clump: Clump loci based on a Linkage Disequilibrium threshold

Description

This function uses clumping to remove SNPs at high LD. When used with its default options, clumping based on MAF is similar to standard pruning (as done by PLINK with "--indep-pairwise (size+1) 1 thr.r2", but it results in a better spread of SNPs over the chromosome. This function is a wrapper around bigsnpr::snp_clumping(). See https://privefl.github.io/bigsnpr/articles/pruning-vs-clumping.html for more information on the differences between pruning and clumping.

Usage

loci_ld_clump(.x, .col = "genotypes", ...)
# S3 method for tbl_df
loci_ld_clump(.x, .col = "genotypes", ...)
# S3 method for vctrs_bigSNP
loci_ld_clump(
  .x,
  .col = "genotypes",
  S = NULL,
  thr_r2 = 0.2,
  size = 100/thr_r2,
  exclude = NULL,
  use_positions = TRUE,
  n_cores = 1,
  return_id = FALSE,
  ...
)

Value

a boolean vector indicating whether the SNP should be kept (if 'return_id = FALSE', the default), else a vector of SNP indices to be kept (if 'return_id = TRUE')

Arguments

.x: a gen_tibble object
.col: the column to be used when a tibble (or grouped tibble is passed directly to the function). This defaults to "genotypes" and can only take that value. There is no need for the user to set it, but it is included to resolve certain tidyselect operations.
...: currently not used.
S: A vector of loci statistics which express the importance of each SNP (the more important is the SNP, the greater should be the corresponding statistic).
For example, if S follows the standard normal distribution, and "important" means significantly different from 0, you must use abs(S) instead.
If not specified, MAFs are computed and used.
thr_r2: Threshold over the squared correlation between two SNPs. Default is 0.2.
size: For one SNP, window size around this SNP to compute correlations. Default is 100 / thr_r2 for clumping (0.2 -> 500; 0.1 -> 1000; 0.5 -> 200). If use_positions = FALSE, this is a window in number of SNPs, otherwise it is a window in kb (genetic distance). Ideally, use positions, as they provide a more sensible approach.
exclude: Vector of SNP indices to exclude anyway. For example, can be used to exclude long-range LD regions (see Price2008). Another use can be for thresholding with respect to p-values associated with S.
use_positions: boolean, if TRUE (the default), size is in kb, if FALSE size is the number of SNPs.
n_cores: number of cores to be used
return_id: boolean on whether the id of SNPs to keep should be returned. It defaults to FALSE, which returns a vector of booleans (TRUE or FALSE)

Details

Any missing values in the genotypes of a gen_tibble passed to loci_ld_clump will cause an error. To deal with missingness, see gt_impute_simple().

Examples

Run this code

if (FALSE) { # all(rlang::is_installed(c("RhpcBLASctl", "data.table")))
# \dontshow{
data.table::setDTthreads(2)
RhpcBLASctl::blas_set_num_threads(2)
RhpcBLASctl::omp_set_num_threads(2)
# }
example_gt <- load_example_gt("gen_tbl") %>% gt_impute_simple()

# To return a boolean vector indicating whether the SNP should be kept
example_gt %>% loci_ld_clump()
# To return a vector of SNP indices to be kept
example_gt %>% loci_ld_clump(return_id = TRUE)
}