tai {CINmetrics}R Documentation

Total Aberration Index

Description

Total Aberration Index calculation takes the sum of lengths of each segment times its segmentation mean for each sample and divides it by the sum of the lengths of each sample.

Usage

tai(cnvData, segmentMean = 0.2, numProbes = NA)

Arguments

cnvData

dataframe containing following columns: Sample, Start, End, Num_Probes, Segment_Mean

segmentMean

numerical value for the minimum segment_mean cutoff/ threshold. Default is 0.2

numProbes

Number of Probes

Details

The Total Aberration Index (TAI) (Baumbusch LO, et. al.) is “a measure of the abundance of genomic size of copy number changes in a tumour". It is defined as a weighted sum of the segment means

Total\ Aberration\ Index = \frac {\sum^{R}_{i = 1} {d_i} \cdot |{\bar{y}_{S_i}}|} {\sum^{R}_{i = 1} {d_i}}\ \ where |\bar{y}_{S_i}| \ge |\log_2 1.7|

Value

Average of lengths weighted by segmentation mean for each unique sample

Examples

tai(cnvData = maskCNV_BRCA)

[Package CINmetrics version 0.1.0 Index]