segFracBSignal: segmentation function for the allele B fraction

Description

This function launches the segmentation of allele B fraction only for heterozygous SNPs.

Usage

segFracBSignal(
  dataSetName,
  normalTumorArray,
  chromosome = 1:22,
  Rho = NULL,
  listOfFiles = NULL,
  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.

Rho

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 allele B profile is segmented (default is all the files).

savePlot

if TRUE, graphics of the segmented allele B profile will be saved in the figures/dataSetName/segmentation/fracB folder. (default=TRUE).

verbose

if TRUE print some informations

Value

a data.frame where each row correspond to a different segment with columns :

sampleNames: The name of the signal.
chromosome: A vector of the same size as copynumber containing the chromosome number.
chromStart: The starting position of a segment.
chromEnd: The ending position of a segment.
probes: The number of probes in the segment.
means: Means of the segment.