CAnD: Perform Chromosomal Ancestry Differences (CAnD) Analyses
Version 1.8.0

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.

AuthorCaitlin McHugh, Timothy Thornton
Bioconductor views GeneticVariability Genetics SNP StatisticalMethod
Date of publicationNone
MaintainerCaitlin McHugh <mchughc@uw.edu>
LicenseArtistic-2.0
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CAnD")

Popular man pages

ancestries: Sample Chromosomal Proportions of Ancestral Subpopulations to...
barPlotAncest: Create a Barplot of Ancestry Proportion Estimates for Every...
calc_combP: Calculate the Combined CAnD Test Statistic P-value
CAnD: Peform the CAnD Test
getDiffMatrices: Calculate the Mean Ancestry Proportion Excluding Each...
plotPvals: Create a Plot of P-Values for Each Chromosome or Chromosomal...
test-method: ~~ Methods for Function 'test' ~~
See all...

All man pages Function index File listing

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' ~~

Functions

BonfCorr Man page
BonfCorr,CAnDResult-method Man page
BonfCorr-methods Man page
CAnD Man page Source code
CAnDResult-class Man page
ancestries Man page
barPlotAncest Man page Source code
calc_combP Man page Source code
getDiffMatrices Man page Source code
overallStatistic Man page
overallStatistic,CAnDResult-method Man page
overallStatistic-methods Man page
overallpValue Man page
overallpValue,CAnDResult-method Man page
overallpValue-methods Man page
pValues Man page
pValues,CAnDResult-method Man page
pValues-methods Man page
plotPvals Man page Source code
test Man page
test,CAnDResult-method Man page
test-methods Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/CAnD-internal.R
R/CAnD.R
R/CAnDResult-accessors.R
R/barPlotAncest.R
R/calc_combP.R
R/getDiffMatrices.R
R/plotPvals.R
R/show-methods.R
build
build/vignette.rds
data
data/ancestries.rda
inst
inst/doc
inst/doc/CAnD.R
inst/doc/CAnD.Rnw
inst/doc/CAnD.pdf
inst/unitTests
inst/unitTests/test_CAnD.R
man
man/BonfCorr-method.Rd
man/CAnD.Rd
man/CAnDResult-class.Rd
man/ancestries.Rd
man/barPlotAncest.Rd
man/calc_combP.Rd
man/getDiffMatrices.Rd
man/overallStatistic-method.Rd
man/overallpValue-method.Rd
man/pValues-method.Rd
man/plotPvals.Rd
man/test-method.Rd
tests
tests/runTests.R
vignettes
vignettes/CAnD.Rnw
CAnD documentation built on May 20, 2017, 10:57 p.m.

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