simer (version 1.0.0)

simer.Data.Geno: 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
)

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.

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.

Author

Dong Yin

Details

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

Examples

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

if (FALSE) {
# It needs "plink" software
simer.Data.Geno(fileBed=fileBed)
}