man/CAFE-package.Rd
ebc089a6
 \name{CAFE-package}
 \alias{CAFE-package}
 \alias{CAFE}
 \docType{package}
 \title{
 Chromosomal Aberrations Finder in Expression data
 }
 \description{
 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).
 }
 \details{
 \tabular{ll}{
 Package: \tab CAFE\cr
 Type: \tab Package\cr
 Version: \tab 0.6.9.5 \cr
 Date: \tab 2013-05-16\cr
 License: \tab GPLv3\cr
 }
 }
 \author{
 Sander Bollen
 }
 \references{
 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
 }
 
 \keyword{ package }
 
 \examples{
 \dontrun{
 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
 
 }
 }