MPAgenomics (version 1.2.3)

getSymFracBSignal: Extract symmetrized allele B fraction signal from aroma files

Description

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

Usage

getSymFracBSignal(
  dataSetName,
  file,
  chromosome,
  normalTumorArray,
  verbose = TRUE
)

Arguments

dataSetName

The name of the data-set folder (it must correpond to a folder name in rawData folder.)

file

The name of the file in dataSetName to extract.

chromosome

A vector with the chromosomes for which the symetrized signal will be extracted.

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.

verbose

If TRUE, print some informations.

Value

a list of length the number of chromosome containing a data.frame with columns:

chromosome

chromosome corresponding to the signal.

position

Positions associated to the allele B fraction.

fracB

One column named by the data file name. It contains the symmetrized allele B fraction signal for the specified profile.

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.

Examples

# NOT RUN {
#DO NOT EXECUTE before reading the vignette
fracB=getSymFracBSignal("data1",5,normalTumorArray)
fracB=getSymFracBSignal("data2",5)
# }
# NOT RUN {
# }