Manuka11: Manuka chromosome 11 SNPs and pedigree file

In tpbilton/GUSMap: Genotyping Uncertainty with Sequencing Data and Linkage Mapping (GUSMap)

Manuka chromosome 11 SNPs and pedigree file

Description

Function for extracting the path to the Variant Call Format (VCF) file of the Manuka data used in the publication by \insertCitebilton2018genetics1;textualGUSMap and a associated pedigree file.

Usage

Manuka11()

Details

The data consists of a full-sib family with 177 progeny and 680 SNPs, genotyped using the genotyping-by-sequencing method. 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. Note that some samples can be from the same individual.

• Mother: The ID of the mother as given in the IndividualID. Note, if the mother is unknown then this should be left blank.

• Father: The ID of the father as given in the IndividualID. Note, if the father is unknown then this should be left blank.

• Family: The name of the Family for a group of progeny with the same parents. Note that this is not necessary but if given must be the same for all the progeny in the same family.

Value

A character string of the complete path to the manuka data set contained in the package and associated pedigree file.

Author(s)

Timothy P. Bilton

References

\insertRef

bilton2018genetics1GUSMap

Examples

## extract the name of the vcf file and the pedigree file
Manuka11()

tpbilton/GUSMap documentation built on Feb. 22, 2025, 12:27 p.m.