CAFE-package {CAFE} | R Documentation

## 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

### Author(s)

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

### 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)

[Package CAFE version 1.23.0 Index]