cape: Combined Analysis of Pleiotropy and Epistasis

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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.

Author
Anna L. Tyler, Wei Lu, Justin J. Hendrick, Vivek M. Philip, and Greg W. Carter
Date of publication
2016-06-09 19:59:15
Maintainer
Anna L. Tyler <Anna.Tyler@jax.org>
License
GPL-3
Version
2.0.2

View on CRAN

Man pages

bin.vector
Bin a continuous vector into discrete values.
calc.delta.errors
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.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'...
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.on.the.fly
Kinship correction for genotype and phenotype.
linkage.blocks.network
Calculates linkage blocks using community detection.
make.data.obj
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.
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...
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
cape/inst
cape/inst/doc
cape/inst/doc/cape.Rnw
cape/inst/doc/cape.pdf
cape/inst/doc/cape.R
cape/NAMESPACE
cape/data
cape/data/obesity.cross.rda
cape/R
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/select.by.chr.R
cape/R/plotVariantInfluences.R
cape/R/read.geno.R
cape/R/plotPairscan.R
cape/R/get.marker.chr.R
cape/R/linkage.blocks.network.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/select.by.ind.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/kinship.on.the.fly.R
cape/R/get.layout.mat.R
cape/R/direct.influence.R
cape/R/qqPheno.R
cape/R/sortCross.R
cape/R/get.network.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/calc.delta.errors.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/get.marker.name.R
cape/R/get.linearly.independent.R
cape/R/make.data.obj.R
cape/R/get.marker.val.R
cape/vignettes
cape/vignettes/interaction_fig.pdf
cape/vignettes/cape.bib
cape/vignettes/cape.Rnw
cape/vignettes/cape-017.pdf
cape/vignettes/reparam.pdf
cape/vignettes/cape-019.pdf
cape/MD5
cape/build
cape/build/vignette.rds
cape/DESCRIPTION
cape/man
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/select.by.ind.Rd
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/linkage.blocks.network.Rd
cape/man/direct.influence.Rd
cape/man/kinship.on.the.fly.Rd
cape/man/consec.pairs.Rd
cape/man/segment.region.Rd
cape/man/pairscan.kin.Rd
cape/man/select.by.chr.Rd
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/calc.delta.errors.Rd
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/get.marker.name.Rd
cape/man/get.network.Rd
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/make.data.obj.Rd
cape/man/remove.ind.Rd
cape/man/sortByThenBy.Rd
cape/man/singlescan.Rd