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 |