How to: Export total copy numbers and allele B fractions as aroma binary data files

Author: Henrik Bengtsson
Created on: 2010-11-04
Last updated: 2010-11-04

The exportTotalAndFracB() method exports Affymetrix-specific copy-number estimates of to a technology-independent data format. The output are so called aroma binary files containing estimates of the total CN signals (not always ratios) and allele B fractions (BAFs). The input data are so called Affymetrix chip-effect estimates in the form of a ChipEffectSet. The output is a list of two elements where the first specifies an AromaUnitTotalCnBinarySet and the second an AromaUnitFracBCnBinarySet.

Usage

dsList <- exportTotalAndFracB(cesN)

Examples

Exporting a chip-effect set containing non-polymorphic (total) and allele B fraction (BAF) estimates

# Setup the chip-effect set (as generated by CRMA v2)
cesN <- SnpChipEffectSet$byName("GSE8605", tags="ACC,-XY,BPN,-XY,AVG,FLN,-XY", chipType="Mapping10K_Xba142")

# Export it
dsList <- exportTotalAndFracB(cesN)
print(dsList)

## $total
## AromaUnitTotalCnBinarySet:
## Name: GSE8605
## Tags: ACC,-XY,BPN,-XY,AVG,FLN,-XY
## Full name: GSE8605,ACC,-XY,BPN,-XY,AVG,FLN,-XY
## Number of files: 10
## Names: GSM226867, GSM226868, ..., GSM226876 [10]
## Path (to the first file):
## totalAndFracBData/GSE8605,ACC,-XY,BPN,-XY,AVG,FLN,-XY/Mapping10K_Xba142
## Total file size: 0.39 MB
## RAM: 0.02MB
## 
## $fracB
## AromaUnitFracBCnBinarySet:
## Name: GSE8605
## Tags: ACC,-XY,BPN,-XY,AVG,FLN,-XY
## Full name: GSE8605,ACC,-XY,BPN,-XY,AVG,FLN,-XY
## Number of files: 10Names: GSM226867, GSM226868, ..., GSM226876 [10]
## Path (to the first file):
## totalAndFracBData/GSE8605,ACC,-XY,BPN,-XY,AVG,FLN,-XY/Mapping10K_Xba142
## Total file size: 0.39 MB
## RAM: 0.01MB