MPAgenomics (version 1.2.3)

cnSegCallingProcess: Segment a copy-number signal and call the found segments.

Description

This function applies the PELT method to segment each signal of the dataset and launches CGHcall for calling segments and detect aberrations. Results will be stored in a text file in the segmentation folder of the aroma architecture.

Usage

cnSegCallingProcess(
  dataSetName,
  normalTumorArray,
  chromosome = 1:22,
  Rho = NULL,
  listOfFiles = NULL,
  onlySNP = TRUE,
  savePlot = TRUE,
  nclass = 3,
  cellularity = 1,
  ...
)

Arguments

dataSetName

name of the data-set folder in the rawData folder containing the signals to use.

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 containing the chromosomes to segment.

Rho

A 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 from the dataSetName to use.

onlySNP

If TRUE, only the SNP probes will be used.

savePlot

If TRUE, save the segmented signal in figures folder.

nclass

The number of levels to be used for calling. Either 3 (loss, normal, gain), 4 (including amplifications), 5 (including double deletions) (default=3).

cellularity

Percentage of tumored cells in the sample (default=1).

...

Other parameters of CGHcall function

Value

a data.frame containg columns :

sampleNames

Name of the file.

chrom

The chromosome of the segment.

chromStart

The starting position (in bp) of a segment. This position is not included in the segment.

chromEnd

The ending position (in bp) of a segment.This position is included in the segment.

probes

Number of probes in the segment.

means

Mean of the segment.

calls

The calling of segment ("double loss", "loss", "normal", "gain" or "amplification").

Examples

# NOT RUN {
#DO NOT EXECUTE before reading the vignette
seg1=cnSegCallingProcess("data1",normalTumorArray,chromosome=20:21)
seg2=cnSegCallingProcess("data2",chromosome=20:21)
# }
# NOT RUN {
# }