R2-D2-model

R2-D2 model is a statistical method to identify the potential regulatory genetic variants to a gene. (add more description here once it is published).

Table of Contents

1. Prepare input files

2. Download the scripts in this repository

3. Run the R2-D2 model

4. Generate R2-D2 plots

5. Example

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Requirements

R version >= 3.3.0

required R packages:

MASS
RcppEigen  
data.table

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Prepare input files

Three types of input files are needed to run this model.

1. Genotype file which describes the SNP genotypes for a group of individuals. It can be generated by PLINK.
2. Phenotype file. This should be three-column text files, of which the first two columns are family ID (FID), and individual IDs (IID), and the third column
3. Genotype-Phenotype association results. This is also a standard output from PLINK. It listed useful metrics of genotype-phenotype associations, such as P-value, R-squared, and direction of effect.

Run the R2-D2 main program

This is done by running the comTest_matrix() function in the protocol.R file

Paramters:

-- geno: the genotype file

-- qassoc: the genotype-phenotype association file

-- num: number of SNPs in a SNP combination to be exaustively tested

-- save_interm: whether or not to save the intermediate files, useful for checking model

comTest_matrix(geno = , qassoc = , num = 4, save_interm = T)

Generate the R2-D2 plots

This is done by running the familyPlot_matrix() function in the protocol.R file

Paramters:

-- plot_file: input file generated by the comTest_matrix()

-- title: title to be displayed in the plots, also used as output filename

-- color: colors for the SNPs chosen by the model.

familyPlot_matrix(plot_file = , title = , color = c("red", "green", "black")) 

Example