taiModified: Modified Total Aberration Index

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

Modified Total Aberration Index

Description

Modified 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

taiModified(cnvData, sample_column = 1, segmentMean = 0, 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

Modified Total Aberration Index uses all sample values instead of those in aberrant copy number state, thus does not remove the directionality from the score.

Modified\ Total\ Aberration\ Index = \frac {\sum^{R}_{i = 1} {d_i} \cdot {\bar{y}_{S_i}}} {\sum^{R}_{i = 1} {d_i}}

Value

Average of lengths weighted by segmentation mean for each unique sample

See Also

tai

Examples

taiModified(cnvData = maskCNV_BRCA)

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