getGenotypeCalls: Extract genotype calls from aroma files
Description
Extract genotype calls 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 genotype call will be extracted.
listOfFiles
A vector containing the names of the files in dataSetName folder for which the genotype signal 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 data.frame with columns:
chromosome
Chromosome of the signal.
position
Positions associated with the genotype.
genotype
Genotype calls corresponding to 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.