epistatic.correlation: Calculate the epistatic interaction effect between SNP pairs...

In victorcarmelo/WISH: Network construction of whole genome genotype data using the WISH network method

Description

A WISH network can be built based on epistatic interaction effects between SNP pairs. Those interaction effects are calculated using linear models.

Usage

epistatic.correlation(phenotype, genotype, parallel,test,simple)

Arguments

phenotype	Dataframe with the rows correspinding to the individuals in the analysis,and columns for the different measured phenotypes and fixed/random factors. Only give one phenotype column at a time. Phenotypes should be continous variables. Make sure that the dataframe contains the same individuals as in the genotype-file, and that those are in the same order.
genotype	Dataframe with the genotype information, resulting from the function generate.genotype(). Make sure that the dataframe contains the same individuals as in the phenotype-file, and that those are in the same order.
parallel	Number of cores to use for parallel execution in the function registerDoParallel()
test	True or False value indicating if a test run is being perform. If True will calculate the expected time it will take for the full analysis based on calculating 100.000 models with the setting chosen
simple	True or false value indicating if only a major/major and minor/minor directed interaction model are tested (simple=T) or if if interactions on the major/minor minor axis are tested as well, with the best one of the two being selected (simple=F).

Value

A list of two matrices. The first matrix gives the epistatic interaction effects between all the SNP-pairs which were in the input genotype data) and selected with the pvalue from the GWAS results. The second matrix are the corresponding pvalues of the parameter estimates of the epistatic interactions.

References

Lisette J.A. Kogelman and Haja N.Kadarmideen (2014). Weighted Interaction SNP Hub (WISH) network method for building genetic networks for complex diseases and traits using whole genome genotype data. BMC Systems Biology 8(Suppl 2):S5. http://www.biomedcentral.com/1752-0509/8/S2/S5.

Examples

epistatic.correlation(phenotype,genotype,parallel,test,simple)

victorcarmelo/WISH documentation built on May 3, 2019, 6:11 p.m.