cape: Combined Analysis of Pleiotropy and Epistasis

Combines complementary information across multiple related phenotypes to infer directed epistatic interactions between genetic markers. This analysis can be applied to a variety of engineered and natural populations.

AuthorAnna L. Tyler, Wei Lu, Justin J. Hendrick, Vivek M. Philip, and Greg W. Carter
Date of publication2016-06-09 19:59:15
MaintainerAnna L. Tyler <>

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Man pages

bin.vector: Bin a continuous vector into discrete values. Error propagation

calc.p: Calculate P Values for Interactions Based on Permutations

cape-package: Combinatorial Analysis of Epistasis and Pleiotropy

consec.pairs: Generate a matrix of consecutive pairs

delete.pheno: Remove phenotypes from the phenotype matrix

direct.influence: Calculate the significance of direct influences of variant...

error.prop: Estimate Errors of Regression Coefficients

filter.hwe: Filter markers by Hardy-Weinberg equilibrium

filter.maf: Filter markers by minor allele frequency.

genome.wide.threshold.1D: Calculate a genome-wide significance threshold for the...

genome.wide.threshold.1D.parallel: Calculate a genome-wide significance threshold for the...

get.chr.markers: Calculate a genome-wide significance threshold for the...

get.col: Retrieve colors for use in plotting.

get.col.num: Use column titles to retrieve column numbers

get.covar: Get information about covariates

get.eigentraits: Calculate eigentraits from phenotype matrix

get.geno: Retrieve the genotype matrix.

get.geno.with.covar: Retrieve the genotype matrix with the covariates appended.

get.layout.mat: Get the best layout matrix for a given number of panes per...

get.linearly.independent: Find all markers in the genotype matrix that are linearly...

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 names from marker numbers

get.marker.num: Get marker numbers from marker names

get.marker.val: Get marker values Convert the final results to a form plotted by 'plotNetwork'...

get.pairs.for.pairscan: Select marker pairs for pairscan based on filters

get.pheno: Retrieve the genotype matrix.

histPheno: Plot histograms of phenotypes.

impute.missing.geno: Impute missing genotypes in measured markers.

kinship: Calculate all leave-one-out or leave-two-out kinship... Kinship correction for genotype and phenotype. Calculates linkage blocks using community detection. Generate data.obj from pheno.obj and geno.obj

marker2covar: Create a covariate from a genetic marker.

myImagePlot: Used in plotting results of pair scan.

norm.pheno: Normalize and mean center phenotypes

obesity.cross: Mouse cross data from Reifsnyder et al. (2000)

one.pairscan.parallel: Perform regression analysis for one phenotype and all pairs...

one.singlescan: Runs one singlescan

pair.matrix: Given a vector of elements, create a two-column matrix...

pairscan: Perform regressions for all pairs of markers and all...

pairscan.kin: Performs a pairscan with kinship correction.

pairscan.noKin: Performs a pairscan without a kinship correction.

pairscan.null: Generate a null distribution for the pairscan.

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...

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

report.progress: Print the progress of a function to the screen

rotate.mat: Rotate a matrix 90 degrees clockwise

rz.transform: Normalize a vector using rank normalization

segment.region: Divide a region into equal parts. Subset a cross object to include only specified chromosomes. 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...

select.pheno: Select phenotypes for analysis

singlescan: Run the single-variant regression for all phenotypes

sortByThenBy: Write out a cape data object to .csv format.

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

Files in this package

cape/R/rotate.mat.R cape/R/remove.ind.R cape/R/consec.pairs.R cape/R/read.pheno.R cape/R/get.marker.num.R cape/R/ cape/R/plotVariantInfluences.R cape/R/read.geno.R cape/R/plotPairscan.R cape/R/get.marker.chr.R cape/R/ cape/R/report.progress.R cape/R/delete.pheno.R cape/R/read.population.R cape/R/pairscan.noKin.R cape/R/get.col.R cape/R/get.marker.idx.R cape/R/plotPhenoCor.R cape/R/writePopulation.R cape/R/pairscan.kin.R cape/R/get.col.num.R cape/R/filter.maf.R cape/R/ cape/R/get.marker.location.R cape/R/plotCollapsedVarInf.R cape/R/pairscan.R cape/R/singlescan.R cape/R/bin.vector.R cape/R/one.pairscan.parallel.R cape/R/sortByThenBy.R cape/R/plotSinglescan.R cape/R/get.pheno.R cape/R/ cape/R/get.layout.mat.R cape/R/direct.influence.R cape/R/qqPheno.R cape/R/sortCross.R cape/R/ cape/R/get.chr.markers.R cape/R/norm.pheno.R cape/R/myImagePlot.R cape/R/get.geno.R cape/R/genome.wide.threshold.1D.R cape/R/writeVariantInfluences.R cape/R/remove.markers.R cape/R/get.geno.with.covar.R cape/R/plotNetwork.R cape/R/rz.transform.R cape/R/select.markers.for.pairscan.R cape/R/get.eigentraits.R cape/R/get.covar.R cape/R/one.singlescan.R cape/R/select.eigentraits.R cape/R/segment.region.R cape/R/pheno2covar.R cape/R/error.prop.R cape/R/impute.missing.geno.R cape/R/plotPheno.R cape/R/histPheno.R cape/R/get.pairs.for.pairscan.R cape/R/genome.wide.threshold.1D.parallel.R cape/R/plotSinglescan.heat.R cape/R/pair.matrix.R cape/R/ cape/R/calc.p.R cape/R/kinship.R cape/R/filter.hwe.R cape/R/marker2covar.R cape/R/pairscan.null.R cape/R/select.pheno.R cape/R/plotSVD.R cape/R/ cape/R/get.linearly.independent.R cape/R/ cape/R/get.marker.val.R
cape/man/get.geno.Rd cape/man/get.layout.mat.Rd cape/man/genome.wide.threshold.1D.Rd cape/man/delete.pheno.Rd cape/man/qqPheno.Rd cape/man/rotate.mat.Rd cape/man/ cape/man/pair.matrix.Rd cape/man/bin.vector.Rd cape/man/histPheno.Rd cape/man/cape-package.Rd cape/man/get.marker.chr.Rd cape/man/error.prop.Rd cape/man/plotVariantInfluences.Rd cape/man/plotPairscan.Rd cape/man/plotPheno.Rd cape/man/get.covar.Rd cape/man/sortCross.Rd cape/man/plotCollapsedVarInf.Rd cape/man/ cape/man/direct.influence.Rd cape/man/ cape/man/consec.pairs.Rd cape/man/segment.region.Rd cape/man/pairscan.kin.Rd cape/man/ cape/man/genome.wide.threshold.1D.parallel.Rd cape/man/get.marker.num.Rd cape/man/select.markers.for.pairscan.Rd cape/man/writeVariantInfluences.Rd cape/man/get.marker.val.Rd cape/man/filter.maf.Rd cape/man/get.geno.with.covar.Rd cape/man/pairscan.noKin.Rd cape/man/pheno2covar.Rd cape/man/select.eigentraits.Rd cape/man/myImagePlot.Rd cape/man/get.pheno.Rd cape/man/ cape/man/remove.markers.Rd cape/man/get.col.Rd cape/man/report.progress.Rd cape/man/kinship.Rd cape/man/impute.missing.geno.Rd cape/man/get.col.num.Rd cape/man/one.singlescan.Rd cape/man/filter.hwe.Rd cape/man/plotSinglescan.Rd cape/man/writePopulation.Rd cape/man/read.pheno.Rd cape/man/pairscan.null.Rd cape/man/get.marker.location.Rd cape/man/plotPhenoCor.Rd cape/man/ cape/man/ cape/man/get.eigentraits.Rd cape/man/rz.transform.Rd cape/man/plotSVD.Rd cape/man/read.geno.Rd cape/man/one.pairscan.parallel.Rd cape/man/get.linearly.independent.Rd cape/man/marker2covar.Rd cape/man/calc.p.Rd cape/man/get.pairs.for.pairscan.Rd cape/man/plotNetwork.Rd cape/man/norm.pheno.Rd cape/man/select.pheno.Rd cape/man/get.marker.idx.Rd cape/man/plotSinglescan.heat.Rd cape/man/read.population.Rd cape/man/obesity.cross.Rd cape/man/pairscan.Rd cape/man/get.chr.markers.Rd cape/man/ cape/man/remove.ind.Rd cape/man/sortByThenBy.Rd cape/man/singlescan.Rd

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