getFracBSignal: Extract allele B fraction signal from aroma files
Description
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.
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).
Value
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.
Details
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.
# NOT RUN {#DO NOT EXECUTE before reading the vignette fracB=getFracBSignal("data1",5,normalTumorArray)
fracB=getFracBSignal("data2",5)
# }# NOT RUN {# }