| 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)