Home

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.