Normalization process

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Description

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

Usage

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SignalNormalization(dataFolder, chipType, normalTumorArray,
  genotypeCallsMethod = "naive", savePlot = TRUE, tags = NULL)

Arguments

dataFolder

Name of the data set.

chipType

Type of the chip used for the data.

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.

genotypeCallsMethod

method used for genotypage, default is "naive".

savePlot

If TRUE, graphics of the CN signal and allele B fraction signal will be saved in the figures 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 aroma architecture must be respected: <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

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

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