Skip to contents

Read Genotype Data

Source: R/class_tassel_genotype.R
readGenotype.Rd

This function reads genotype data from a file path or an R matrix. It supports optional sorting of positions and retaining depth information.

Usage

readGenotype(x, sortPositions = FALSE, keepDepth = FALSE)

Arguments

x

A character string representing the file path to the genotype data or a matrix containing genotype data.

sortPositions

A logical value indicating whether to sort positions in the genotype data. Default is FALSE.

keepDepth

A logical value indicating whether to retain depth information in the genotype data. Default is FALSE.

Value

A processed genotype object based on the input data.

Details

  • If x is a character string:

    • The function checks if the file exists.

    • Reads the genotype data from the file path using readGenotypeFromPath.

  • If x is a matrix:

    • The function processes the genotype data using readGenotypeFromRMatrix.

  • If x is neither a character string nor a matrix:

    • An error is raised.

Examples

if (FALSE) { # \dontrun{
# Read genotype data from a file
readGenotype("path/to/genotype/file.txt", sortPositions = TRUE, keepDepth = TRUE)

# Read genotype data from a matrix
genotypeMatrix <- matrix(data = ..., nrow = ..., ncol = ...)
readGenotype(genotypeMatrix)
} # }