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

Export total copy numbers and allele B fractions as aroma binary data sets

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 (previously generated by CRMAv2)
cesN <- SnpChipEffectSet$byName("GSE8605", tags="ACC,-XY,BPN,-XY,AVG,FLN,-XY", chipType="Mapping10K_Xba142");

# Export it
dsList <- exportTotalAndFracB(cesN, verbose=verbose);
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: 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: 0.01MB

$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