simer.Data.Ped: Pedigree data quality control

In simer: Data Simulation for Life Science and Breeding

Pedigree data quality control

Description

Data quality control for pedigree data.

Usage

simer.Data.Ped(
  filePed,
  fileMVP = NULL,
  out = NULL,
  standardID = FALSE,
  fileSir = NULL,
  fileDam = NULL,
  exclThres = 0.1,
  assignThres = 0.05,
  header = TRUE,
  sep = "\t",
  ncpus = 0,
  verbose = TRUE
)

Arguments

filePed	the filename of pedigree need correcting.
fileMVP	genotype in MVP format.
out	the prefix of output file.
standardID	whether kid id is 15-character standard.
fileSir	the filename of candidate sires.
fileDam	the filename of candidate dams.
exclThres	if conflict ratio is more than exclThres, exclude this parent.
assignThres	if conflict ratio is less than assignThres, assign this parent to the individual.
header	whether the file contains header.
sep	separator of the file.
ncpus	the number of threads used, if NULL, (logical core number - 1) is automatically used.
verbose	whether to print detail.

Details

Build date: May 6, 2021 Last update: Apr 28, 2022

Value

the function returns files

<out>.ped.report

the report file containing correction condition.

<out>.ped.error

the file containing pedigree error.

<out>.ped

the pedigree file after correction.

Author(s)

Lilin Yin and Dong Yin

Examples

# Get the filename of pedigree data
filePed <- system.file("extdata", "05others", "pedigree.txt", package = "simer")

# Get the prefix of genotype data
fileMVP <- system.file("extdata", "01bigmemory", "demo", package = "simer")

# Run pedigree correction
simer.Data.Ped(filePed = filePed, fileMVP = fileMVP, out = tempfile("outfile"))

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