setupGADA: Imports array data (pennCNV format) to R-GADA

In isglobal-brge/R-GADA: Genome Alteration Detection Algorithm (GADA)

Description

This function encapsulates information in pennCNV format to be analyzed with R-GADA

Usage

setupGADA(file, MarkerIdCol=1, ChrNameCol=2, ChrPosCol=3,
          log2ratioCol, BAFcol, chrs = c(1:22, "X", "Y"),
          XY=TRUE, sort = TRUE, orderProbes, gen.info, 
          saveGenInfo = TRUE) 

Arguments

file	A file with Illumina data (obtained from BeadStudio)
MarkerIdCol	The column in 'file' containing the name of the marker
ChrNameCol	The column in 'file' containing the chromosome
ChrPosCol	The column in 'file' containing the genomic position
log2ratioCol	The column in 'file' containing log2ratio intensities
BAFcol	The column in 'file' containing B-allele freqencies
chrs	A vector containg the available chromosomes. The default is c(1:22, "X", "Y")
XY	Do data have X and Y labels in annotation (instead of 23 and 24)? The default is TRUE
sort	Should data be sorted using genomic information? The default is TRUE
orderProbes	Used to avoid sorting
gen.info	genomic information. Not required
saveGenInfo	Should annotation data be saved? The default is TRUE. See details

Details

The arguments 'orderProbes' and 'saveGenInfo' should not be changed by the user.

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, 2010;11:380.

Examples

 ## Not run: 
  See the vignette
 
## End(Not run) 

isglobal-brge/R-GADA documentation built on May 24, 2019, 5:03 a.m.