# Combined Analysis of Pleiotropy and Epistasis

## Documentation for package ‘cape’ version 2.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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
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
filter.hwe | Filter markers by Hardy-Weinberg equilibrium
filter.maf | Filter markers by minor allele frequency.
get.covar | Get information about covariates
get.eigentraits | Calculate eigentraits from phenotype matrix
get.geno | Retrieve the genotype matrix.
get.marker.chr | Get chromosome assignments for a vector of markers.
get.marker.idx | Get the column index of markers in the genotype matrix
get.marker.location | Get the chromosomal coordinate of markers
get.marker.name | Get marker names from marker numbers
get.marker.num | Get marker numbers from marker names
get.marker.val | Get marker values
get.network | Convert the final results to a form plotted by 'plotNetwork' and 'plotCollapsedVarInf'
get.pheno | Retrieve the genotype matrix.
histPheno | Plot histograms of phenotypes.
impute.missing.geno | Impute missing genotypes in measured markers.
make.data.obj | Generate data.obj from pheno.obj and geno.obj
marker2covar | Create a covariate from a genetic marker.
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.
pheno2covar | Create a covariate from a phenotype.
plotCollapsedVarInf | Plot variant-to-variant influences
plotNetwork | Plot the final epistatic network
plotPairscan | plot the results from 'pairscan'
plotPheno | Plot phenotype values by individual.
plotPhenoCor | Plot correlations between phenotype pairs.
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
qqPheno | Plot qq plots of phenotype pairs.
read.geno | Read in and format data for analysis by 'cape'
read.pheno | Read in and format data for analysis by 'cape'
read.population | Read in and format data for analysis by 'cape'
remove.ind | Remove individuals from the data.obj
remove.markers | Remove markers from the data.obj
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
singlescan | Run the single-variant regression for all phenotypes
sortCross | Sort the genetic markers in the data.obj.
writePopulation | Write out a cape data object to .csv format.
writeVariantInfluences | Write the final results to a file