SignalNormalization {MPAgenomics} | R Documentation |
low-level normalization process for estimating raw copy-numbers and allele B fraction.
SignalNormalization(dataFolder, chipType, normalTumorArray, genotypeCallsMethod = "naive", savePlot = TRUE, tags = NULL)
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. |
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
Quentin Grimonprez