How to: Calculate total copy number ratios from from total (non-polymorphic) signals

Author: Henrik Bengtsson
Created on: 2011-12-03
Last updated: 2011-12-03

Copy-number (CN) preprocessing method such as doCRMAv2() and doASCRMAv2() outputs total signals for each locus. These signals are not CN ratios, but only signals that are not comparable across loci, meaning they cannot be segmented. In order to obtain total CNs (TCN), we need to calculate the ratios for these signals relative to corresponding signals of a reference. For instance, for a tumor the reference can be a matched normal. Another choice of reference is a robust average of a large pool of samples. This section describes how to calculate total CN ratios relative to a reference.

Setting up an already preprocessed data set

Assume that a CEL data set named 'MyDataSet' has previously been processed by doCRMAv2() and afterward R was quit. To access the results, which was automatically stored on the file system, do:

dataSet <- "MyDataSet"
tags <- "ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY";  # Tags added by CRMA v2
chipType <- "GenomeWideSNP_6"
ds <- AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags, chipType=chipType)

so that print(ds) gives:

AromaUnitTotalCnBinarySet:
Name: MyDataSet
Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
Full name: MyDataSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
Number of files: 12
Names: GSA2031T,
GSA2031N, GSA2032T, GSA2032N, ... [12]
Path (to the first file):
totalAndFracBData/MyDataSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
Total file size: 21.53 MB
RAM: 0.00MB

Generating paired total copy numbers

In order to calculated paired total copy numbers (TCN), that is, TCN ratios of tumors relative to their matched normals, we first need to match up the tumor and normals by placing the in two separate data sets and making sure their ordering matches. Then we can use exportTotalCnRatioSet() to calculate the TCNs for us. For example:

# Extract the tumors
dsT <- ds[indexOf(ds, pattern="T$")]

# Extract the normals
dsN <- ds[indexOf(ds, pattern="N$")]

# We will assume that the names matches
stopifnot(gsub("T$", getNames(dsT)) == gsub("N$", getNames(dsN)))

# Calculate TCNs
dsTN <- exportTotalCnRatioSet(dsT, ref=dsN)

Generating total copy numbers relative to pool of all samples

In order to calculate paired TCNs relative to the average of a set of reference samples, do:

# Use the normals as the reference set
dsN <- ds[indexOf(ds, pattern="N$")]

# Calculate the average normal
dfR <- getAverageFile(dsN)

# Calculate TCNs
dsTR <- exportTotalCnRatioSet(dsT, ref=dfR)