Overview
Mendel Location Scores is a component of the umbrella OpenMendel project. This package performs multipoint linkage analysis. That is, the analysis considers multiple linked markers in combination when mapping the trait.
Appropriate Problems and Data Sets
Mendel Location Scores analysis can use sib pairs, nuclear families, or large pedigrees, along with marker and trait data, to localize genes.
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 MendelLocationScores:
pkg> add https://github.com/OpenMendel/MendelLocationScores.jl.git
This package supports Julia v1.0+
Input Files
The MendelLocationScores analysis package uses the following input files. Example input files can be found in the data subfolder of the MendelLocationScores 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 Location Scores:
#
# Input and Output files.
#
locus_file = location scores LocusFrame.txt
pedigree_file = location scores PedigreeFrame.txt
phenotype_file = location scores PhenotypeFrame.txt
output_file = location scores Output.txt
lod-score-table = location scores Table Output.txt
#
# Analysis parameters for Location Scores option.
#
trait = RADIN
travel = grid
gender-neutral = false
In the example above, there are eight keywords. Three keywords specify the input files: location scores LocusFrame.txt, location scores PedigreeFrame.txt, and location scores PhenotypeFrame.txt. The next two keywords specify the output files: location scores Output.txt the results file - and location scores Table Output.txt - a table of the location scores. The last three keywords specify analysis parameters. The text after the ‘=’ are the keyword values.
Keywords
This is a list of OpenMendel keywords specific to Location Scores. 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 |
|---|---|---|---|
| flanking_distance | [0.5, 0.5] | Real | Marker flanking distance for location scores |
| flanking_markers | 1 | Integer | Number of flanking markers in imputation window |
| gender_neutral | TRUE | TRUE, FALSE | Whether different male/female recombination fractions are considered |
| lod_score_table | “Lod_Score_Frame.txt” | User defined output text file name | Creates a lod score table output file |
Data Files
Location Scores requires a Control file, and a Pedigree file. Genotype data are provided in a SNP data file, with a SNP Definition File describing the SNPs. 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 Location Scores data folder.
Running the Analysis
To run this analysis package, first launch Julia. Then load the package with the command:
julia> using MendelLocationScores
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> LocationScores("Control_file.txt")
Note: The package is called MendelLocationScores but the analysis function is called simply LocationScores.
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.