Man pages for cape
Combined Analysis of Pleiotropy and Epistasis

bin.vectorBin a continuous vector into discrete values. propagation
calc.pCalculate P Values for Interactions Based on Permutations
cape-packageCombinatorial Analysis of Epistasis and Pleiotropy
consec.pairsGenerate a matrix of consecutive pairs
delete.phenoRemove phenotypes from the phenotype matrix
direct.influenceCalculate the significance of direct influences of variant...
error.propEstimate Errors of Regression Coefficients
filter.hweFilter markers by Hardy-Weinberg equilibrium
filter.mafFilter markers by minor allele frequency.
genome.wide.threshold.1DCalculate a genome-wide significance threshold for the...
genome.wide.threshold.1D.parallelCalculate a genome-wide significance threshold for the...
get.chr.markersCalculate a genome-wide significance threshold for the...
get.colRetrieve colors for use in plotting.
get.col.numUse column titles to retrieve column numbers
get.covarGet information about covariates
get.eigentraitsCalculate eigentraits from phenotype matrix
get.genoRetrieve the genotype matrix.
get.geno.with.covarRetrieve the genotype matrix with the covariates appended.
get.layout.matGet the best layout matrix for a given number of panes per...
get.linearly.independentFind all markers in the genotype matrix that are linearly...
get.marker.chrGet chromosome assignments for a vector of markers.
get.marker.idxGet the column index of markers in the genotype matrix
get.marker.locationGet the chromosomal coordinate of markers
get.marker.nameGet marker names from marker numbers
get.marker.numGet marker numbers from marker names
get.marker.valGet marker values
get.networkConvert the final results to a form plotted by 'plotNetwork'...
get.pairs.for.pairscanSelect marker pairs for pairscan based on filters
get.phenoRetrieve the genotype matrix.
histPhenoPlot histograms of phenotypes.
impute.missing.genoImpute missing genotypes in measured markers.
kinshipCalculate all leave-one-out or leave-two-out kinship...
kinship.on.the.flyKinship correction for genotype and phenotype.
linkage.blocks.networkCalculates linkage blocks using community detection. data.obj from pheno.obj and geno.obj
marker2covarCreate a covariate from a genetic marker.
myImagePlotUsed in plotting results of pair scan.
norm.phenoNormalize and mean center phenotypes
obesity.crossMouse cross data from Reifsnyder et al. (2000)
one.pairscan.parallelPerform regression analysis for one phenotype and all pairs...
one.singlescanRuns one singlescan
pair.matrixGiven a vector of elements, create a two-column matrix...
pairscanPerform regressions for all pairs of markers and all...
pairscan.kinPerforms a pairscan with kinship correction.
pairscan.noKinPerforms a pairscan without a kinship correction.
pairscan.nullGenerate a null distribution for the pairscan.
pheno2covarCreate a covariate from a phenotype.
plotCollapsedVarInfPlot variant-to-variant influences
plotNetworkPlot the final epistatic network
plotPairscanplot the results from 'pairscan'
plotPhenoPlot phenotype values by individual.
plotPhenoCorPlot correlations between phenotype pairs.
plotSinglescanPlot the results of singlescan
plotSinglescan.heatPlot the results of singlescan as a heatmap
plotSVDPlot the results of the singular value decomposition of the...
plotVariantInfluencesPlot variant-to-variant influences
qqPhenoPlot qq plots of phenotype pairs.
read.genoRead in and format data for analysis by 'cape'
read.phenoRead in and format data for analysis by 'cape'
read.populationRead in and format data for analysis by 'cape'
remove.indRemove individuals from the data.obj
remove.markersRemove markers from the data.obj
report.progressPrint the progress of a function to the screen
rotate.matRotate a matrix 90 degrees clockwise
rz.transformNormalize a vector using rank normalization
segment.regionDivide a region into equal parts. a cross object to include only specified chromosomes. a cross object to include specific individuals
select.eigentraitsSelect a subset of the eigentraits for further analysis
select.markers.for.pairscanA required step that filters variable and non-redundant...
select.phenoSelect phenotypes for analysis
singlescanRun the single-variant regression for all phenotypes
sortByThenByWrite out a cape data object to .csv format.
sortCrossSort the genetic markers in the data.obj.
writePopulationWrite out a cape data object to .csv format.
writeVariantInfluencesWrite the final results to a file
cape documentation built on May 2, 2019, 3:27 a.m.