simer.Data.Impute: Genotype data imputation

In simer: Data Simulation for Life Science and Breeding

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
)

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.

Details

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

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.

Author(s)

Dong Yin

Examples

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

## Not run: 
# It needs 'beagle' software
fileMVPimp <- simer.Data.Impute(fileBed = fileBed)

## End(Not run)

simer documentation built on April 3, 2025, 9:24 p.m.