This function launches the segmentation process using the aroma architecture.
segmentationAroma(
dataSetName,
normalTumorArray,
chromosome = 1:22,
Rho = NULL,
listOfFiles = NULL,
onlySNP = TRUE,
savePlot = TRUE,
verbose = TRUE
)
The name of the data-set folder (it must correspond to a folder name in rawData folder.).
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.
A vector with the chromosomes to be segmented.
A vector containing all the penalization values to test for the segmentation. If no values are provided, default values will be used.
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).
If TRUE, only the copy-number for SNPs positions will be returned (default=TRUE).
if TRUE, graphics of the segmented CN signal will be saved in the figures/dataSetName/segmentation/CN folder. (default=TRUE).
if TRUE print some informations
a list containing
A vector containing the copynumber signal.
A vector of the same size as copynumber containing the segmented values.
The position of each probes.
A vector of the same size as copynumber containing the chromosome number.
Names of the probes.
The name of the signal.
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.