SignalNormalization: Normalization process

In MPAgenomics: Multi-Patient Analysis of Genomic Markers

Description

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

Usage

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

Value

No return value, called for side effects.

Author(s)

Quentin Grimonprez

MPAgenomics documentation built on March 30, 2021, 5:13 p.m.