segmentationAroma: segmentation function
In sblanck/MPAgenomics: Multi-Patient Analysis of Genomic Markers

Description Usage Arguments Value Author(s)

This function launches the segmentation process using the aroma architecture.

segmentationAroma(
  dataSetName,
  normalTumorArray,
  chromosome = 1:22,
  method = c("PELT", "cghseg"),
  Kmax,
  Rho = NULL,
  listOfFiles = NULL,
  onlySNP = TRUE,
  savePlot = TRUE,
  verbose = TRUE
)

`dataSetName`	The name of the data-set folder (it must correspond to a folder name in rawData folder.).
`normalTumorArray`	Only in the case of normal-tumor study. A csv file or a data.frame containing the mapping between normal and tumor files The first column contains the name of normal files and the second the names of associated tumor files.
`chromosome`	A vector with the chromosomes to be segmented.
`method`	method of segmentation, either "PELT" or "cghseg".
`Kmax`	For method="cghseg", maximal number of segments.
`Rho`	For method="PELT", vector containing all the penalization values to test for the segmentation. If no values are provided, default values will be used.
`listOfFiles`	A vector containing the names of the files in dataSetName folder for which the copy number profiles will be segmented (default is all the files).
`onlySNP`	If TRUE, only the copy-number for SNPs positions will be returned (default=TRUE).
`savePlot`	if TRUE, graphics of the segmented CN signal will be saved in the figures/dataSetName/segmentation/CN folder. (default=TRUE).
`verbose`	if TRUE print some informations

a list containing

copynumber: A vector containing the copynumber signal.
segmented: A vector of the same size as copynumber containing the segmented values.
startPos: The position of each probes.
chromosome: A vector of the same size as copynumber containing the chromosome number.
featureNames: Names of the probes.
sampleNames: The name of the signal.
segment: A data.frame that summarizes the results of the segmentation. Each row is a different segment with the chromosome, start position, end position, number of probes in the signal and the value of the segment.