CAFE-package: Chromosomal Aberrations Finder in Expression data
In CAFE: Chromosmal Aberrations Finder in Expression data

Description Details Author(s) References Examples

CAFE attempts to find chromosomal aberrations in microarray expression (mRNA) data. It contains several plotting functions to aid in visualizing these aberrations. It generally recapitulates the workflow described by Mayshar et al (see references), and implements several algorithms described by Friedrich et al (see references).

Package:	CAFE
Type:	Package
Version:	0.6.9.5
Date:	2013-05-16
License:	GPLv3

Sander Bollen

Friedrich, F., Kempe, a, Liebscher, V., & Winkler, G. (2008). Complexity Penalized M-Estimation. Journal of Computational and Graphical Statistics, 17(1), 201-224. doi:10.1198/106186008X285591

Mayshar, Y., Ben-David, U., Lavon, N., Biancotti, J.-C., Yakir, B., Clark, A. T., Plath, K., et al. (2010). Identification and classification of chromosomal aberrations in human induced pluripotent stem cells. Cell stem cell, 7(4), 521-31. doi:10.1016/j.stem.2010.07.017

## Not run: 
setwd("/some/path/to/cel/files")
data <- ProcessCels() 
# process cel files
samples <- c(1,2) 
# select samples 1 and 2 to compare against the rest
chromosomeStats(data,chromNum="ALL",samples=samples) 
# check for chromosomal gains
chromosomeStats(data,chromNum="ALL",samples=samples,alternative="less") 
# check for chromosomal losses
bandStats(data,chromNum=1,samples=samples) 
# check for band gains in chr1
bandStats(data,chromNum=1,samples=samples,alternative="less") 
# check for band losses in chr1
rawPlot(data,chromNum=1,samples=samples,idiogram=TRUE) 
# plot raw data with an ideogram
slidPlot(data,chromNum=1,samples=samples,idiogram=TRUE,combine=TRUE,k=100) 
# moving average plot with ideogram
discontPlot(data,chromNum=1,samples=samples,idiogram=TRUE) 
# discontinuous plot with ideogram


## End(Not run)