simer (version 1.0.0)

simer.Data.Impute: Genotype data imputation

Description

Impute the missing value within genotype data.

Usage

simer.Data.Impute(
  fileMVP = NULL,
  fileBed = NULL,
  out = NULL,
  maxLine = 10000,
  ncpus = 0,
  verbose = TRUE
)

Value

the function returns files

<out>.geno.desc

the description file of genotype data.

<out>.geno.bin

the binary file of genotype data.

<out>.geno.ind

the genotyped individual file.

<out>.geno.map

the marker information data file.

Arguments

fileMVP

genotype in MVP format.

fileBed

genotype in PLINK binary format.

out

the name of output file.

maxLine

number of SNPs, only used for saving memory when calculate kinship matrix.

ncpus

the number of threads used, if NULL, (logical core number - 1) is automatically used.

verbose

whether to print detail.

Author

Dong Yin

Details

Build date: May 26, 2021 Last update: Apr 28, 2022

Examples

# Get the prefix of genotype data
fileMVP <- system.file("extdata", "02plinkb", "demo", package = "simer")

if (FALSE) {
# It needs 'beagle' software
fileMVPimp <- simer.Data.Impute(fileBed = fileBed)
}