simer (version 1.0.0)

simer.Data.Pheno: Phenotype data quality control

Description

Data quality control for phenotype data.

Usage

simer.Data.Pheno(
  filePhe = NULL,
  filePed = NULL,
  out = NULL,
  planPhe = NULL,
  pheCols = NULL,
  header = TRUE,
  sep = "\t",
  missing = c(NA, "NA", "Na", ".", "-", "NAN", "nan", "na", "N/A", "n/a", "", "",
    "-9", 9999),
  verbose = TRUE
)

Value

the function returns files

<out>.phe

the phenotype file after correction.

Arguments

filePhe

the phenotype files, it can be a vector.

filePed

the pedigree files, it can be a vector.

out

the prefix of output file.

planPhe

the plans for phenotype quality control.

pheCols

the column needing extracting.

header

the header of file.

sep

the separator of file.

missing

the missing value.

verbose

whether to print detail.

Author

Haohao Zhang and Dong Yin

Details

Build date: June 13, 2021 Last update: Apr 28, 2022

Examples

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

# Run phenotype correction
simer.Data.Pheno(filePhe = filePhe, out = tempfile("outfile"))