mice_impute: Imputation via mice
In surh/HMVAR: Human Microbiome Variant Analysis in R

Imputes missing genotypes using mice

mice_impute(
  geno,
  snp,
  outdir = "imputed/",
  m = 5,
  verbose = FALSE,
  prefix = "imputed",
  return_table = FALSE,
  seed = NA,
  block_size = 100
)

`geno`	A data table with genotype information. First three columns must be site_id, minor_allele and major allele; folowed by one column per sample with the sample ID as column name. Missing genotypes must be encoded as NA values
`snp`	SNP information data table. Must have columns ID, pos and chr. ID mut correspond to the "site_id" column in `geno`, and the SNPs must be in the same order in both tables.
`outdir`	Output directory to create and write the imputed table in BIMBAM format.
`m`	Number of multiple imputations. See mice documentation.
`verbose`	Whether to print progress during imputation.
`prefix`	Prefix for imputed file.
`return_table`	If TRUE, the function will return a list with both the output file path and the imputed table. If FALSE, only the file path will be returned.
`seed`	Seed for imputation. See mice documentation.
`block_size`	Number of markers to use to impute each marker.