segmentationAroma {MPAgenomics}R Documentation

segmentation function

Description

This function launches the segmentation process using the aroma architecture.

Usage

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

Arguments

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

Value

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.

Author(s)

Quentin Grimonprez


[Package MPAgenomics version 1.1.6 Index]