cna: Copy Number Aberration

In CINmetrics: Calculate Chromosomal Instability Metrics

Description

Calculates the number of copy number aberrations

Usage

cna(
  cnvData,
  segmentMean = (log(1.7, 2) - 1),
  numProbes = NA,
  segmentDistance = 0.2,
  minSegSize = 10
)

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
segmentDistance	Segment distance threshold
minSegSize	Minimum segment size

Details

Copy Number Aberrations (CNA) (Davidson JM, et al), are defined as a segment with copy number outside the pre-defined range of 1.7-2.3

(\log_2 1.7 -1) ≤ \bar{y}_{S_i} ≤ (\log_2 2.3 -1)

that is not contiguous with an adjacent independent CNA of identical copy number. For our purposes, we have adapted the range to be

|\bar{y}_{S_i}| ≥ |\log_2 1.7|

, which is only slightly larger than the original. It is nearly identical to countingBreakPoints, except this one calculates breaks as adjacent segments that have a difference in segment means of ≥ 0.2.

Total\ Copy\ Number\ Aberration = ∑^{R}_{i = 1} n_i \ where \ \bar{y}_{S_i}| ≥ |\log_2{1.7}|, \ \bar{y}_{S_{i-1}} - \bar{y}_{S_i}| ≥ 0.2, \ d_i ≥ 10

Value

Number of copy number aberrations between segments

See Also

countingBreakPoints

Examples

cna(cnvData = maskCNV_BRCA)

CINmetrics documentation built on Aug. 2, 2021, 9:06 a.m.