Combined Analysis of Pleiotropy and Epistasis


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Documentation for package ‘cape’ version 2.0.2

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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
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