Functions to perform the CAnD test on a set of ancestry proportions. For a particular ancestral subpopulation, a user will supply the estimated ancestry proportion for each sample, and each chromosome or chromosomal segment of interest. A p-value for each chromosome as well as an overall CAnD p-value will be returned for each test. Plotting functions are also available.

Author | Caitlin McHugh, Timothy Thornton |

Date of publication | None |

Maintainer | Caitlin McHugh <mchughc@uw.edu> |

License | Artistic-2.0 |

Version | 1.6.0 |

**ancestries:** Sample Chromosomal Proportions of Ancestral Subpopulations to...

**barPlotAncest:** Create a Barplot of Ancestry Proportion Estimates for Every...

**BonfCorr-method:** ~~ Methods for Function 'BonfCorr' ~~

**calc_combP:** Calculate the Combined CAnD Test Statistic P-value

**CAnD:** Peform the CAnD Test

**CAnDResult-class:** Class '"CAnDResult"'

**getDiffMatrices:** Calculate the Mean Ancestry Proportion Excluding Each...

**overallpValue-method:** ~~ Methods for Function 'overallpValue' ~~

**overallStatistic-method:** ~~ Methods for Function 'overallStatistic' ~~

**plotPvals:** Create a Plot of P-Values for Each Chromosome or Chromosomal...

**pValues-method:** ~~ Methods for Function 'pValues' ~~

**test-method:** ~~ Methods for Function 'test' ~~

CAnD/DESCRIPTION

CAnD/NAMESPACE

CAnD/R

CAnD/R/AllClasses.R
CAnD/R/AllGenerics.R
CAnD/R/CAnD-internal.R
CAnD/R/CAnD.R
CAnD/R/CAnDResult-accessors.R
CAnD/R/barPlotAncest.R
CAnD/R/calc_combP.R
CAnD/R/getDiffMatrices.R
CAnD/R/plotPvals.R
CAnD/R/show-methods.R
CAnD/build

CAnD/build/vignette.rds

CAnD/data

CAnD/data/ancestries.rda

CAnD/inst

CAnD/inst/doc

CAnD/inst/doc/CAnD.R

CAnD/inst/doc/CAnD.Rnw

CAnD/inst/doc/CAnD.pdf

CAnD/inst/unitTests

CAnD/inst/unitTests/test_CAnD.R

CAnD/man

CAnD/man/BonfCorr-method.Rd
CAnD/man/CAnD.Rd
CAnD/man/CAnDResult-class.Rd
CAnD/man/ancestries.Rd
CAnD/man/barPlotAncest.Rd
CAnD/man/calc_combP.Rd
CAnD/man/getDiffMatrices.Rd
CAnD/man/overallStatistic-method.Rd
CAnD/man/overallpValue-method.Rd
CAnD/man/pValues-method.Rd
CAnD/man/plotPvals.Rd
CAnD/man/test-method.Rd
CAnD/tests

CAnD/tests/runTests.R

CAnD/vignettes

CAnD/vignettes/CAnD.Rnw

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