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CNVassoc (version 1.4)

Association analysis of CNV data

Description

This package carries out association analysis of common copy number variants in population-based studies. This package includes functions for analysing association under a series of study designs (case-control, cohort, etc), using several dependent variables (class status, censored data, counts) as response, adjusting for covariates and considering various inheritance models. It also includes functions for inferring copy number (CNV genotype calling). Various classes and methods for generic functions (print, summary, plot, anova, ... ) have been created to facilitate the analysis.

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Version

Install

install.packages('CNVassoc')

Monthly Downloads

50

Version

1.4

License

GPL (>= 2)

Maintainer

Juan Gonzalez

Last Published

September 14th, 2012

Functions in CNVassoc (1.4)

A112

Copy Number Variant intensity data (from CNVtools)
getProbs

Get posterior probabilities from an object of class 'cnv' or 'CGHcall'
CNVassoc-internal

Internal CNVassoc functions
simCNVdataPois

Simulate Poisson data
getProbsRegions

Get posterior probabilities for blocks/regions
NeveRegions

Breast Cancer aCGH data with CGHcall
CNVassoc

Association analysis between a CNV and phenotype
getPvalBH

Corrected p values using Benjamini & Hochberg approach
SNPTEST

Case-control data with SNPTEST format
CNVtest

Testing association between a CNV and phenotype
cnv

CNV object
simCNVdataBinary

Simulation of CNV and discrete traits
simCNVdataCaseCon

Simulation of CNV in a case-control study design
simCNVdataWeibull

Simulate of CNV and a right censored Weibull distributed trait
dataMLPA

MLPA data
NeveCalled

Breast Cancer aCGH data with CGHcall
simCNVdataNorm

Simulation of CNV and quantitative traits
multiCNVassoc

Association between several CNVs and disease
getQualityScore

Computes a quality score for a CNV fit
plotSignal

plots the intensities of a CNV univariate signal data
NeveData

Breast Cancer aCGH data