MPAgenomics (version 1.2.3)

getCopyNumberSignal: Extract copy-number signal from aroma files

Description

Extract copy-number signals from aroma files. It requires to have executed the normalization process suggested by aroma packages, by using signalPreProcess for example.

Usage

getCopyNumberSignal(
  dataSetName,
  chromosome,
  normalTumorArray,
  onlySNP = FALSE,
  listOfFiles = NULL,
  verbose = TRUE
)

Arguments

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 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.

onlySNP

If TRUE, only the copy-number for SNPs positions will be returned (default=FALSE).

listOfFiles

A vector containing the names of the files in dataSetName folder for which the copy-number 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 data.frame with columns:

chromosome

Chromosome of the signal.

position

Positions associated with the copy-number.

copynumber

Copy number 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.

Examples

# NOT RUN {
#DO NOT EXECUTE before reading the vignette
  C=getCopyNumberSignal("data1",5,normalTumorArray,TRUE)
  C=getCopyNumberSignal("data2",5,onlySNP=TRUE)
# }