simer.Data.Impute {simer} | R Documentation |
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)
[Package simer version 0.9.0.4 Index]