simulate_illumina_file: Simulate an Illumina File

In Qploidy: Estimation of Ploidy and Detection of Aneuploidy Using Genotyping Data

Simulate an Illumina File

Description

This function generates a simulated Illumina file with SNP data for a specified number of SNPs and samples. The file includes a header section and a data section with fields such as SNP Name, Sample ID, GC Score, Theta, X, Y, X Raw, Y Raw, and Log R Ratio.

Usage

simulate_illumina_file(
  filepath,
  num_snps = 10,
  num_samples = 1,
  sample_id_prefix = "SAMP",
  mk_id = "MK-",
  seed = 123
)

Arguments

filepath	The path where the simulated Illumina file will be saved. Default is "simulated_summary.txt".
num_snps	The number of SNPs to simulate. Default is 10.
num_samples	The number of samples to simulate. Default is 1.
sample_id_prefix	The prefix for sample IDs. Default is "SAMP".
mk_id	The prefix for marker IDs. Default is "MK-".
seed	The seed for random number generation to ensure reproducibility. Default is 123.

Details

The simulated data includes random values for GC Score, Theta, X, Y, X Raw, Y Raw, and Log R Ratio. The header section provides metadata about the file, including the number of SNPs and samples.

Value

None. The function writes the simulated Illumina file to the specified path.

Qploidy documentation built on June 8, 2025, 10 a.m.