simer.Data.Geno: Genotype data quality control

In simer: Data Simulation for Life Science and Breeding

Genotype data quality control

Description

Data quality control for genotype data in MVP format and PLINK format.

Usage

simer.Data.Geno(
  fileMVP = NULL,
  fileBed = NULL,
  filePlinkPed = NULL,
  filePed = NULL,
  filePhe = NULL,
  out = "simer.qc",
  genoType = "char",
  filter = NULL,
  filterGeno = NULL,
  filterHWE = NULL,
  filterMind = NULL,
  filterMAF = NULL,
  ncpus = 0,
  verbose = TRUE
)

Arguments

fileMVP	genotype in MVP format.
fileBed	genotype in PLINK binary format.
filePlinkPed	genotype in PLINK numeric format.
filePed	the filename of pedigree data.
filePhe	the filename of phenotype data, it can be a vector.
out	the prefix of output files.
genoType	type parameter in bigmemory, genotype data. The default is char, it is highly recommended *NOT* to modify this parameter.
filter	filter of genotyped individual.
filterGeno	threshold of sample miss rate.
filterHWE	threshold of Hardy-Weinberg Test.
filterMind	threshold of variant miss rate.
filterMAF	threshold of Minor Allele Frequency.
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>.bed

the .bed file of PLINK binary format.

<out>.bim

the .bim file of PLINK binary format.

<out>.fam

the .fam file of PLINK binary format.

Author(s)

Dong Yin

Examples

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

## Not run: 
# It needs "plink" software
simer.Data.Geno(fileBed=fileBed)

## End(Not run)

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