segmentationAroma {MPAgenomics} | R Documentation |
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
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.
Quentin Grimonprez