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How to: Setting up an AromaUnitTotalCnBinarySet or an AromaUnitFracBCnBinarySet

Author: Henrik Bengtsson
Created on: 2010-10-24
Last updated: 2010-10-24

An AromaUnitTotalCnBinarySet is a data set than consists of AromaUnitTotalCnBinaryFile:s, which are binary data files holding total copy-number signals independent of technology. That is, an AromaUnitTotalCnBinarySet can hold total CN data from Affymetrix, Illumina, Agilent etc. Analogously, AromaUnitFracBCnBinarySet holds so called allele B fraction CN signals specific to SNP technologies.

This how-to page describes how to setup an AromaUnitTotalCnBinarySet. It does not show how to create/import/allocate/populate such a data set. For that see dedicated page in the How tos section.

Setting up an AromaUnitTotalCnBinarySet

dataSet <- "HapMap270,6.0,CEU,testSet"
tags <- "ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY"
chipType <- "GenomeWideSNP_6"

ds <- AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags, chipType=chipType)
print(ds)

## AromaUnitTotalCnBinarySet:
## Name: HapMap270
## Tags: 6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
## Full name: HapMap270,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
## Number of files: 3
## Names: NA06991, NA06993, NA07000 [3]
## Path (to the first file):
## totalAndFracBData/HapMap270,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
## Total file size: 21.53 MB
## RAM: 0.00MB

An AromaUnitTotalCnBinarySet can for instance be passed to segmentation models, e.g. CbsModel.

Setting up an AromaUnitFracBCnBinarySet

An AromaUnitFracBCnBinarySet can be setup analogously.