CAnD

This package is for version 3.10 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see CAnD.

Perform Chromosomal Ancestry Differences (CAnD) Analyses


Bioconductor version: 3.10

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

Maintainer: Caitlin McHugh <mchughc at uw.edu>

Citation (from within R, enter citation("CAnD")):

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CAnD")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CAnD")
Detecting heterogenity in population structure across chromosomes with the "CAnD" package PDF R Script
Reference Manual PDF

Details

biocViews GeneticVariability, Genetics, SNP, Software, StatisticalMethod
Version 1.18.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License Artistic-2.0
Depends
Imports methods, ggplot2, reshape
System Requirements
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Suggests RUnit, BiocGenerics, BiocStyle
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CAnD_1.18.0.tar.gz
Windows Binary CAnD_1.18.0.zip
Mac OS X 10.11 (El Capitan) CAnD_1.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CAnD
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CAnD
Bioc Package Browser https://code.bioconductor.org/browse/CAnD/
Package Short Url https://bioconductor.org/packages/CAnD/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive