setupGADAgeneral: Imports general array data to gada

In gada: Genome Alteration Detection Algorithm (GADA)

Description

This function encapsulates information obtained from any platform to be analyzed with gada

Usage

setupGADAgeneral(log.ratio, genotype = NULL, B.allele.freq = NULL, gen.info = NULL, type = "log.ratio", sort = FALSE)

Arguments

log.ratio	A vector with log2ratio intensities
genotype	A vector with genotypes. Not required
B.allele.freq	A vector with B-allele frequency. Not required
gen.info	A vector with annotation data. Not required. See details
type	Type of data. By default is 'log.ratio'
sort	Should data be sorted using annotation data given in 'gen.info'

Details

Annotation data if available can be added through the argument 'gen.info' as a data.frame. The following format is required:

        probe chr    pos
1  rs12354060   1  10004
2   rs6650104   1 554340
3  rs12184279   1 707348
4  rs12564807   1 724325
5   rs3115860   1 743268
6   rs7515489   1 758845
7  rs17160939   1 773886
8  rs12086311   1 798632
9   rs4475691   1 836671
10 rs28705211   1 890368
...

Value

An object of class 'setupGADA'

References

Pique-Regi R, Caceres A, Gonzalez JR. "R-Gada: a package for fast detection and visualization of copy number alterations on multiple samples", BMC Bioinformatics , Submitted Nov 2009

See Also

setupGADAIllumina, setupGADAaffy

Examples

## Not run: 
## Simulated data
set.seed(123456)
cn<-rep(c(rep(1,1E5-100),rep(1,100),rep(1,1E5)),4) #Underlying copy number
arrayData<-rnorm(length(cn),mean=(log2(cn)-1),sd=1) #Simulated array

gen.info <- data.frame( probe=paste("id",1:length(cn),sep=""),
            chr=c(rep(1,2E5),rep(2,2E5),rep(3,2E5),rep(4,2E5)),
            pos=rep(1:(length(cn)/4),4)*10)

## setupGADA object with annotation information
dataSim<-setupGADAgeneral(arrayData,gen.info=gen.info)
dataSim

## End(Not run)

gada documentation built on May 2, 2019, 6:10 p.m.