simer.Data.Ped {simer}

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"))