Overview
Mendel Two Point Linkage is a component of the umbrella OpenMendel project. This analysis option maps a trait locus using two-point linkage analysis.
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 MendelTwoPointLinkage:
pkg> add https://github.com/OpenMendel/MendelTwoPointLinkage.jl.git
This package supports Julia v1.0+
Input Files
The Mendel Two Point Linkage analysis package uses the following input files. Example input files can be found in the data subfolder of the Mendel Two Point Linkage 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.
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 Two Point Linkage:
#
# Input and Output files.
#
locus_file = two-point linkage LocusFrame.txt
pedigree_file = two-point linkage PedigreeFrame.txt
phenotype_file = two-point linkage PhenotypeFrame.txt
output_file = two-point linkage Output.txt
lod-score-table = two-point linkage LOD Table Output.txt
#
# Analysis parameters for Two-Point Linkage option.
#
trait = RADIN
gender-neutral = true
standard_errors = true
travel = grid
In the example above, there are nine keywords. The first three keywords specify input files: two-point linkage LocusFrame.txt, two-point linkage PedigreeFrame.txt, two-point linkage PhenotypeFrame.txt. The next two keywords specify output files with results of the analysis: two-point linkage Output.txt and two-point linkage LOD Table Output.txt. The last four keywords specify analysis parameters: disease_status, gender-neutral, standard_errors and travel. The text after the ‘=’ are the keyword values.
Keywords
This is a list of OpenMendel keywords specific to Two Point Linkage. 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 |
|---|---|---|---|
| gender_neutral | true | true, false | Forces equal recombination fractions |
| goal | maximize | ||
| lod_score_table | Lod_Score_Frame.txt | User-defined output file name | Creates a lod score table output file |
| output_unit | |||
| parameters | 1 | ||
| points | 9 | ||
| travel | grid | Mode of sampling parameter space |
Data Files
Two Point Linkage 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 Two Point Linkage data folder.
Running the Analysis
To run this analysis package, first launch Julia. Then load the package with the command:
julia> using MendelTwoPointLinkage
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> TwoPointLinkage("Control_file.txt")
Note: The package is called MendelTwoPointLinkage but the analysis function is called simply TwoPointLinkage.
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.