writeResults {ADaCGH}R Documentation

Write results to an external file

Description

Write segmentation results to an external file, including original information (name, chromosome, position, log-ratio) and assigned state and/or smoothed mean (depending on what is available from the method). (In addition, a set of files with links to PaLS http://pals.bioinfo.cnio.es will be generated when there is state information.)

Usage

writeResults(obj, ...)
## S3 method for class 'CGH.PSW':
writeResults(obj, commondata, file = "PSW.output.txt", ...)
## S3 method for class 'summaryACE':
writeResults(obj, acghdata, commondata, file = NULL, ...)
## S3 method for class 'CGH.wave':
writeResults(obj, acghdata, commondata,
                     file = "wavelet.output.txt", ...)
## S3 method for class 'DNAcopy':
writeResults(obj, acghdata, commondata, 
                     file = "CBS.output.txt", ...)
## S3 method for class 'CGHseg':
writeResults(obj, acghdata, commondata, 
                     file = "CGHseg.output.txt", ...)
## S3 method for class 'mergedHMM':
writeResults(obj, acghdata, commondata, 
                     file = "HMM.output.txt", ...)
## S3 method for class 'adacghGLAD':
writeResults(obj, acghdata, commondata,
                     file = "GLAD.output.txt", ...)
## S3 method for class 'mergedBioHMM':
writeResults(obj, acghdata, commondata, 
                     file = "BioHMM.output.txt", ...)

Arguments

obj The output object from previous analysis; in all cases, the output from pSegement except for ACE, where it is the output from summary.
file The name of the output file.
acghdata The aCGH data set; see pSegmentWavelets.
commondata The common data; see common.data in pSegmentPSW.
... Other arguments passed to the underlying functions.

Value

A file is written in your system with columns corresponding to the original data (including ID, Chromosome, etc) and the results of the segmentations.

Author(s)

Ramon Diaz-Uriarte rdiaz02@gmail.com

References

Diaz-Uriarte, R. and Rueda, O.M. (2006). ADaCGH: an R package and web-based application for the analysis of aCGH data. Tech. report. http://www.ligarto.org/rdiaz/Papers/adacgh.pdf, http://adacgh.bioinfo.cnio.es.

See Also

pSegmentACE, pSegmentWavelets, pSegmentPSW, pSegmentDNAcopy, summary.ACE,

Examples

## See examples under pSegmentDNAcopy

[Package ADaCGH version 1.3-10 Index]