getFracBSignal: Extract allele B fraction signal from aroma files
In MPAgenomics: Multi-Patient Analysis of Genomic Markers

Description Usage Arguments Details Value Author(s) Examples

Extract allele B fraction signals from aroma files. It requires to have executed the normalization process suggested by aroma packages, by using signalPreProcess for example.

getFracBSignal(
  dataSetName,
  chromosome,
  normalTumorArray,
  listOfFiles = NULL,
  verbose = TRUE
)

`dataSetName`	The name of the data-set folder (it must correspond to a folder name in rawData folder.)
`chromosome`	A vector containing the chromosomes for which the allele B fraction signal must be extract.
`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.
`listOfFiles`	A vector containing the names of the files in dataSetName folder for which the allele B fraction profiles will be extracted (default is all the files).
`verbose`	If TRUE print some information (default=TRUE).

The aroma architecture must be respected. The working directory must contain rawData folder and totalAndFracBData folder. To easily access the names of the files available in a dataset, one can use the getListOfFiles function.

a list of length the number of chromosomes containing a list of two elements (normal and tumor) containing a data.frame with columns:

chromosome: Chromosome of the signal.
position: Positions associated with the allele B fraction.
fracB: Allele B fraction profiles of selected files; the name of each column is the name of the associated data file name.
featureNames: Names of the probes.

Quentin Grimonprez

## Not run: 
#DO NOT EXECUTE before reading the vignette
  fracB=getFracBSignal("data1",5,normalTumorArray)
  fracB=getFracBSignal("data2",5)

## End(Not run)