CAnD: Perform Chromosomal Ancestry Differences (CAnD) Analyses

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

View on Bioconductor

Man pages

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' ~~

Files in this package

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