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CNVassoc (version 1.0)

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 generic functions (print, summary, plot, anova, ... ) have been created to facilitate the analysis.

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Version

Install

install.packages('CNVassoc')

Monthly Downloads

20

Version

1.0

License

GPL (>= 2)

Maintainer

Juan Gonzalez

Last Published

April 26th, 2011

Functions in CNVassoc (1.0)

CNVtest

Testing association between a CNV and phenotype
A112

Copy Number Variant intensity data (from CNVtools)
CNVassoc-internal

Internal CNVassoc functions
NeveData

Breast Cancer aCGH data
getPvalBH

Corrected p values using Benjamini & Hochberg approach
simCNVdataBinary

Simulation of CNV and discrete traits
simCNVdataPois

Simulate Poisson data
getQualityScore

Computes a quality score for a CNV fit
getProbsRegions

Get posterior probabilities for blocks/regions
SNPTEST

Case-control data with SNPTEST format
plotSignal

plots the intensities of a CNV univariate signal data
dataMLPA

MLPA data
cnv

CNV object
simCNVdataWeibull

Simulate of CNV and a right censored Weibull distributed trait
simCNVdataCaseCon

Simulation of CNV in a case-control study design
NeveRegions

Breast Cancer aCGH data with CGHcall
CNVassoc

Association analysis between a CNV and phenotype
getProbs

Get posterior probabilities from an object of class 'cnv' or 'CGHcall'
simCNVdataNorm

Simulation of CNV and quantitative traits
multiCNVassoc

Association between several CNVs and disease
NeveCalled

Breast Cancer aCGH data with CGHcall