signalPreProcess: Normalization process

In MPAgenomics: Multi-Patient Analysis of Genomic Markers

Description

normalization process for estimating raw copy-numbers and allele B fraction.

Usage

signalPreProcess(dataSetName, chipType, normalTumorArray, dataSetPath,
  chipFilesPath = dataSetPath, path = ".", createArchitecture = TRUE,
  savePlot = TRUE, tags = NULL)

Arguments

dataSetName	Name of the data set. If you use architecture=FALSE, the name must correspond to a name of folder in the rawData folder.
chipType	Type of the used chip (e.g. "GenomeWideSNP_6"). If architecture=FALSE, the files of the chip must be contained in the annotationData folder, if TRUE, they have to be in the "chipTypePath" folder.
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.
dataSetPath	(only if createArchitecture=TRUE) Path to the folder containing the CEL files of the data-set.
chipFilesPath	(only if createArchitecture=TRUE) Path to the folder containing all the annotations files for the specified chip type.
path	(only if createArchitecture=TRUE) Path where the architecture should be created (default=".").
createArchitecture	if TRUE, the aroma architecture will be automatically created (default=TRUE). CEL files of the data and chip files will be copied (not moved).
savePlot	if TRUE, graphics of the CN signal and allele B fraction signal will be saved in the figures/signal folder.
tags	Common tag which appears in the different file names (cdf, ugp, ufl) of the chip. For no tag, use tags=NULL (default = NULL). See details for more information.

Details

The following architecture must be used: <working directory> +- annotationData/ | +- chipTypes/ | +- <chipType>/ <– must match exactly the name of the CDF file (fullname minus tags) | +- CDF file(s) and other annotation (possibly subdirectories) | +- rawData/ +- <nameOfDataSet>/ +- <chipType>/ <– must match exactly a chip type folder under annotationData/ +- CEL files

If you use createArchitecture=TRUE, this function creates this architecture for you and copy your files in the right folders.

The functions will create other folders which contain figures, results of normalization.

If you already have the required architecture, you just have to add your data in the rawData folder with respect to the architecture.

All the cdf chip file names must follow the following rule : <chipType>,<Tags>.cdf

Multiples tags must be separated by a comma. If there is no tag, the pattern is <chipType>.cdf

Author(s)

Quentin Grimonprez

MPAgenomics documentation built on Jan. 16, 2020, 3 p.m.