simer.Data: Data handling
In simer: Data Simulation for Life Science and Breeding

simer.Data

R Documentation

Data handling

Description

Make data quality control for genotype, phenotype, and pedigree.

Usage

simer.Data(jsonList = NULL, out = "simer.qc", ncpus = 0, verbose = TRUE)

Arguments

`jsonList`	a list of data quality control parameters.
`out`	the prefix of output files.
`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 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

# Read JSON file
jsonFile <- system.file("extdata", "04breeding_plan", "plan1.json", package = "simer")
jsonList <- jsonlite::fromJSON(txt = jsonFile, simplifyVector = FALSE)

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

## End(Not run)

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