low-level normalization process for estimating raw copy-numbers and allele B fraction.
SignalNormalization(
dataFolder,
chipType,
normalTumorArray,
genotypeCallsMethod = "naive",
savePlot = TRUE,
tags = NULL
)Name of the data set.
Type of the chip used for the data.
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.
method used for genotypage, default is "naive".
If TRUE, graphics of the CN signal and allele B fraction signal will be saved in the figures folder.
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.
No return value, called for side effects.
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