create_knockoffs: Create Multiple Knockoffs for Genetic Data

In CoxMK: A Model-X Knockoff Method for Genome-Wide Survival Association Analysis

Create Multiple Knockoffs for Genetic Data

Description

Generate knockoff variables for genotype data using the Multiple knockoff method with leveraging scores and clustering specifically optimized for genetic variant data.

Usage

create_knockoffs(
  X,
  pos,
  chr_info = NULL,
  sample_ids = NULL,
  M = 5,
  save_gds = TRUE,
  output_dir = NULL,
  start = NULL,
  end = NULL,
  corr_max = 0.75,
  maxN_neighbor = Inf,
  maxBP_neighbor = 1e+05,
  n_AL = floor(10 * nrow(X)^(1/3) * log(nrow(X))),
  thres_ultrarare = 25,
  R2_thres = 1,
  prob_eps = 1e-12,
  irlba_maxit = 1500
)

Arguments

X	A sparse matrix (n x p) of genotype data where n is the number of samples and p is the number of SNPs. Typically coded as 0, 1, 2 for genotype dosages.
pos	A numeric vector of SNP positions (in base pairs) for linkage disequilibrium-aware knockoff generation.
chr_info	Optional chromosome information. Can be either: (1) A data frame with chromosome information from BIM file containing a column named "chr" or "CHR" with chromosome numbers, or (2) A vector of chromosome numbers directly. Chromosome information will be automatically extracted.
sample_ids	A character vector of sample IDs (default: NULL, will generate)
M	Number of knockoff copies to generate (default: 5). More copies can improve statistical power but increase computational cost.
save_gds	Whether to save knockoffs to GDS format (default: TRUE)
output_dir	Directory to save GDS files (default: NULL, uses tempdir())
start	Start position for file naming (default: min(pos))
end	End position for file naming (default: max(pos))
corr_max	Maximum correlation threshold for clustering variants (default: 0.75). Higher values create fewer, larger clusters.
maxN_neighbor	Maximum number of neighboring variants to consider for each variant (default: Inf).
maxBP_neighbor	Maximum base pair distance to consider variants as neighbors (default: 100,000 bp).
n_AL	Number of samples to use for adaptive lasso fitting (default: automatically determined based on sample size).
thres_ultrarare	Minimum minor allele count threshold for variant inclusion (default: 25).
R2_thres	R-squared threshold for model fitting (default: 1).
prob_eps	Minimum probability value to prevent numerical issues (default: 1e-12).
irlba_maxit	Maximum iterations for truncated SVD (default: 1500).

Value

If save_gds is TRUE, returns the path to the saved GDS file. Otherwise, returns a list of M matrices, each of the same dimensions as X, containing knockoff variables.

CoxMK documentation built on Sept. 9, 2025, 5:24 p.m.