snp_fastImputeSimple: Fast imputation

In bigsnpr: Analysis of Massive SNP Arrays

Fast imputation

Description

Fast imputation via mode, mean, sampling according to allele frequencies, or 0.

Usage

snp_fastImputeSimple(
  Gna,
  method = c("mode", "mean0", "mean2", "random"),
  ncores = 1
)

Arguments

Gna	A FBM.code256 (typically ⁠<bigSNP>$genotypes⁠). You can have missing values in these data.
method	Either "random" (sampling according to allele frequencies), "mean0" (rounded mean), "mean2" (rounded mean to 2 decimal places), "mode" (most frequent call).
ncores	Number of cores used. Default doesn't use parallelism. You may use bigstatsr::nb_cores().

Value

A new FBM.code256 object (same file, but different code).

See Also

snp_fastImpute()

Examples

bigsnp <- snp_attachExtdata("example-missing.bed")
G <- bigsnp$genotypes
G[, 2]  # some missing values
G2 <- snp_fastImputeSimple(G)
G2[, 2]  # no missing values anymore
G[, 2]  # imputed, but still returning missing values
G$copy(code = CODE_IMPUTE_PRED)[, 2]  # need to decode imputed values

G$copy(code = c(0, 1, 2, rep(0, 253)))[, 2]  # "imputation" by 0

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