CAFE (version 1.8.0)

CAFE-package: 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

Package:

CAFE

Type:

Package

Version:

0.6.9.5

Date:

2013-05-16

License:

GPLv3

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

Examples

## 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)