writeResults {ADaCGH} | R Documentation |
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.)
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", ...)
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. |
A file is written in your system with columns corresponding to the original data (including ID, Chromosome, etc) and the results of the segmentations.
Ramon Diaz-Uriarte rdiaz02@gmail.com
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.
pSegmentACE
, pSegmentWavelets
,
pSegmentPSW
, pSegmentDNAcopy
,
summary.ACE
,
## See examples under pSegmentDNAcopy