CAnD

DOI: 10.18129/B9.bioc.CAnD    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see CAnD.

Perform Chromosomal Ancestry Differences (CAnD) Analyses

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	GeneticVariability, Genetics, SNP, Software, StatisticalMethod
Version	1.14.0
In Bioconductor since	BioC 3.1 (R-3.2) (4 years)
License	Artistic-2.0
Depends
Imports	methods, ggplot2, reshape
LinkingTo
Suggests	RUnit, BiocGenerics, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	CAnD_1.14.0.tar.gz
Windows Binary	CAnD_1.14.0.zip
Mac OS X 10.11 (El Capitan)	CAnD_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CAnD
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CAnD
Package Short Url	http://bioconductor.org/packages/CAnD/
Package Downloads Report	Download Stats