simer.Data.Json: Data quality control

In simer: Data Simulation for Life Science and Breeding

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
)

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.

Details

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

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.

Author(s)

Dong Yin

Examples

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

## Not run: 
# It needs "plink" and "hiblup" software
jsonList <- simer.Data.Json(jsonFile = jsonFile)

## End(Not run)

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