simDS: Simulated dataset and pedigree file

In tpbilton/GUSbase: Genotyping Uncertainty with Sequencing Data: Base Package

Simulated dataset and pedigree file

Description

Function for extracting the path to the Variant Call Format (VCF) file of a simulated dataset and associated pedigree file.

Usage

simDS()

Details

The data set consists of a simulated F1 family of 100 progeny, 1000 SNPs and three chromosomes. The data is in VCF format (see this page for specification of VCF format). The pedigree file contains five columns, namely

• SampleID: A unique character string of the sample ID. These correspond to those found in the VCF file

• IndividualID: A character giving the ID number of the individual for which the sample corresponds to.

• Mother: The ID of the mother as given in the IndividualID. Blank fields means the mother is unknown.

• Father: The ID of the father as given in the IndividualID. Blank fields means the father is unknown.

• Family: The name of the Family for a group of progeny with the same parents.

Value

A character string of the complete path to the simulated dataset contained in the package and a pedigree file that goes with the data.

Author(s)

Timothy P. Bilton

Examples

## extract the name of the vcf file and the pedigree file
simDS()

tpbilton/GUSbase documentation built on March 8, 2024, 1:35 p.m.