simer (version 1.0.0)

simer.Data.Json: Data quality control

Description

Make data quality control by JSON file.

Usage

simer.Data.Json(
  jsonFile,
  hiblupPath = "",
  out = "simer.qc",
  dataQC = TRUE,
  buildModel = TRUE,
  buildIndex = TRUE,
  ncpus = 10,
  verbose = TRUE
)

Value

the function returns a list containing

$genotype

the path of genotype data.

$pedigree

the filename of pedigree data.

$selection_index

the selection index for all traits.

$breeding_value_index

the breeding value index for all traits.

$quality_control_plan

a list of parameters for data quality control.

$breeding_plan

a list of parameters for genetic evaluation.

Arguments

jsonFile

the path of JSON file.

hiblupPath

the path of HIBLUP software.

out

the prefix of output files.

dataQC

whether to make data quality control.

buildModel

whether to build EBV model.

buildIndex

whether to build Selection Index.

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: Oct 19, 2020 Last update: Apr 28, 2022

Examples

# Get JSON file
jsonFile <- system.file("extdata", "04breeding_plan", "plan1.json", package = "simer")

if (FALSE) {
# It needs "plink" and "hiblup" software
jsonList <- simer.Data.Json(jsonFile = jsonFile)
}