rCGH-package: Comprehensive Pipeline for Analyzing and Visualizing...
In rCGH: Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

Description Author(s) See Also Examples

A comprehensive pipeline for analyzing and interactively visualizing genomic profiles generated through commercial or custom aCGH arrays. As inputs, rCGH supports Agilent dual-color Feature Extraction files (.txt), from 44 to 400K, Affymetrix SNP6.0 and cytoScanHD probeset.txt, cychp.txt, and cnchp.txt files exported from ChAS or Affymetrix Power Tools.
rCGH also supports custom arrays, provided data is in a suitable format. This package takes over all the steps required for individual genomic profiles analysis, from reading files to segmenting and annotating genes. This package provides several visualization functions (static or interactive) which facilitate individual profiles interpretation. Input files can be in compressed format, e.g. .bz2 or .gz.

Frederic Commo <frederic.commo@gustaveroussy.fr>

readAgilent, readAffySNP6, readAffyCytoScan, readGeneric

filePath <- system.file("extdata", "Affy_cytoScan.cyhd.CN5.CNCHP.txt.bz2",
    package = "rCGH")
cgh <- readAffyCytoScan(filePath, sampleName = "AffyScHD")

cgh <- adjustSignal(cgh, nCores=1)
cgh <- segmentCGH(cgh, nCores=1)
cgh <- EMnormalize(cgh)

# Static visalizations
plotDensity(cgh)
multiplot(cgh)

## Not run: 
# Interactive visalizations
view(cgh)

## End(Not run)