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: Specifies the names of your data input and output files and any optional parameters (keywords) for the analysis. (For a list of common keywords, see Keywords Table).
- Locus File: Names and describes the genetic loci in your data.
- Pedigree File: Gives information about your individuals, such as name, sex, family structure, and ancestry.
- Phenotype File: Lists the available phenotypes.
- SNP Definition File: Defines your SNPs with information such as SNP name, chromosome, position, allele names, allele frequencies.
- SNP Data File: Holds the genotypes for your data set. Must be a standard binary PLINK BED file in SNP major format. If you have a SNP data file you must have a SNP definition file.
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.