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MendelKinship.jl

This analysis option computes kinship and other identity coefficients.

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Overview

Mendel Kinship is a component of the umbrella OpenMendel project. Kinship coefficients quantify the degree of relationship between two relatives. Mendel Kinship computes global kinship coefficients and local kinship coefficients. (Global kinship coefficients are also known as theoretical; local are also known as empirical or conditional.) A global kinship coefficient between two individuals i and j is the probability that at an arbitrary locus a randomly sampled gene from i is identical by descent to a randomly sampled gene from j.

Appropriate Problems and Data Sets

Global kinship coefficients based solely on pedigree structure can be quickly computed on pedigrees of all sizes, since marker data are ignored. For any local or SNP-based kinship analysis, avoid mixing autosomal and X-linked loci. Both sets of loci can be analyzed, but they must be run separately. For standard, text-based input files, local kinship analyses will be likelihood-based. For such analyses, including comparing the local to global kinship coefficients, large pedigrees will be bypassed. For binary data files, the SNP-based global and local methods will be used.

Installation

Note: The three OpenMendel packages (1) SnpArrays, (2) MendelSearch, and (3) MendelBase must be installed before any other OpenMendel package will run. It is easiest if these three packages are installed in the above order and before any other OpenMendel package.

Within Julia, use the package manager to install MendelKinship:

pkg> add https://github.com/OpenMendel/MendelKinship.jl.git

This package supports Julia v1.0+

Input Files

The Mendel Kinship analysis package uses the following input files. Example input files can be found in the data subfolder of the Mendel Kinship project. (An analysis won’t always need every file type below.)

Control file

The Control file is a text file consisting of keywords and their assigned values. The format of the Control file is:

Keyword = Keyword_Value(s)

Below is an example of a simple Control file to run Kinship:

#
# Input and Output files.
#
pedigree_file = kinship_PedigreeFrame.txt
kinship_output_file = kinship_file_Output.txt
output_file = kinship_Output.txt
#
# Analysis parameters for Kinship option.
#
repetitions = 1000

In the example above, there are four keywords. The first keyword specifies the input Pedigree file: kinship_PedigreeFrame.txt. The next two keywords specify output files with results of the analysis: kinship_file_Output.txt and kinship_Output.txt. The last keyword specifies the analysis parameter: repetitions. The text after the ‘=’ are the keyword values.

Keywords

This is a list of OpenMendel keywords specific to Kinship. A list of OpenMendel keywords common to most analysis package can be found here. The names of keywords are not case sensitive. (The keyword values may be case sensitive.)

Keyword Default Value Allowed Values Short Description
kinship_output_file Kinship_Output_File.txt User defined output file name OpenMendel generated output file with table of kinship coefficients
repetitions 1 integer Repetitions for sharing statistics
xlinked_analysis FALSE TRUE, FALSE Whether or not markers are on the X chromosome

Data Files

Kinship requires a Control file, and a Pedigree file. Genotype data can be included in the Pedigree file, in which case a Locus file is required. Alternatively, genotype data can be provided in a SNP data file, in which case a SNP Definition File is required. OpenMendel will also accept PLINK format FAM and BIM files. Details on the format and contents of the Control and data files can be found on the MendelBase documentation page. There are example data files in the Kinship data folder.

Running the Analysis

To run this analysis package, first launch Julia. Then load the package with the command:

 julia> using MendelKinship

Next, if necessary, change to the directory containing your files, for example,

 julia> cd("~/path/to/data/files/")

Finally, to run the analysis using the parameters in your Control file, for example, Control_file.txt, use the command:

 julia> Kinship("Control_file.txt")

Note: The package is called MendelKinship but the analysis function is called simply Kinship.

Citation

If you use this analysis package in your research, please cite the following reference in the resulting publications:

OPENMENDEL: a cooperative programming project for statistical genetics. Zhou H, Sinsheimer JS, Bates DM, Chu BB, German CA, Ji SS, Keys KL, Kim J, Ko S, Mosher GD, Papp JC, Sobel EM, Zhai J, Zhou JJ, Lange K. Hum Genet. 2019 Mar 26. doi: 10.1007/s00439-019-02001-z. [Epub ahead of print] PMID: 30915546

Acknowledgments

This project is supported by the National Institutes of Health under NIGMS awards R01GM053275 and R25GM103774 and NHGRI award R01HG006139.