tai: Total Aberration Index

In lasseignelab/CINmetrics: An R package for analyzing copy number aberrations as a measure of chromosomal instability

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, sample_column = 1, segmentMean = 0.2, numProbes = NA)

Arguments

cnvData	dataframe containing following columns: Sample, Start, End, Num_Probes, Segment_Mean
sample_column	numerical value for the sample column number, default is 1
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)

lasseignelab/CINmetrics documentation built on March 23, 2023, 10:38 p.m.