Combined analysis of pleiotropy and epistasis


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Documentation for package ‘cape’ version 1.3

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cape-package Combinatorial Analysis of Epistasis and Pleiotropy
calc.p Calculate P Values for Interactions Based on Permutations
cape Combinatorial Analysis of Epistasis and Pleiotropy
create.covar Designate a phenotype or treatment as a covariate
delete.pheno Remove phenotypes from the phenotype matrix
direct.influence Calculate the significance of direct influences of variant pairs on phenotypes
error.prop Estimate Errors of Regression Coefficients
get.covar Use a threshold to automatically select covariates for the pairscan
get.eigentraits Calculate eigentraits from phenotype matrix
get.network Convert the final results to a form plotted by 'plotNetwork' and 'plotCollapsedVarInf'
norm.pheno Normalize and mean center phenotypes
obesity.cross Mouse cross data from Reifsnyder et al. (2000)
pairscan Perform regressions for all pairs of markers and all phenotypes.
plotCollapsedVarInf Plot variant-to-variant influences
plotNetwork Plot the final epistatic network
plotPairscan plot the results from 'pairscan'
plotSinglescan Plot the results of singlescan
plotSinglescan.heat Plot the results of singlescan as a heatmap
plotSVD Plot the results of the singular value decomposition of the phenotype matrix
plotVariantInfluences Plot variant-to-variant influences
read.population Read in and format data for analysis by 'cape'
select.by.chr Subset a cross object to include only specified chromosomes.
select.by.ind Subset a cross object to include specific individuals
select.eigentraits Select a subset of the eigentraits for further analysis
select.markers.for.pairscan A required step that filters variable and non-redundant markers for the pairscan
select.pheno Select phenotypes for analysis
set.covar Manually set which markers will be used as covariates.
set.pairscan.thresh Manually set the threshold by which markers are selected for the pair scan
singlescan Run the single-variant regression for all phenotypes
writePopulation Write out a cape data object to .csv format.
writeVariantInfluences Write the final results to a file