focalCall (version 1.6.0)

igvFiles: Match Ensembl genes to focal aberrations.

Description

Generates three tracks that can be loaded into IGV (). 1) Segmented data per sample 2) frequency plot based on the calls from CGHcall 3) Frequency plot of focal aberrations as generated with focalCall.

Usage

igvFiles(CGHset)

Arguments

CGHset

Object of class focalCall, contains focalCall output.

Value

Three IGV readable files are returned - Frequency aberrations, Frequency focal aberrations and all segmented values for all samples.

• "FrequencyPlot.igv" is a IGV readable files and contains the frequency plot of all samples and all aberrations.
• "FrequencyPlotfocals.igv" is a IGV readable files and contains the frequency plot of all samples and all focal aberrations.
• "Overview_segments.igv" is a IGV readable files and contains the segmentation log2ratio values.

Details

igvFocal is applied to a (as returned by focalCall version 0.0.99 or higher).

References

Krijgsman O., Benner C., Meijer G.A., Van de Wiel, M.A., Ylstra, B. (2013), "FocalCall: an R-package to detect genomic focal aberrations.", Submitted

See Also

focalCall, CGHcall

Examples

data(BierkensCNA)

# generate IGV readable files
igvFiles(calls_focals)