Combined Analysis of Pleiotropy and Epistasis

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 |

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