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.

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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


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


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

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