simer.Data {simer}

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)