cna {CINmetrics}

Copy Number Aberration

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) \le \bar{y}_{S_i} \le (\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}| \ge |\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 \ge 0.2.

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

Value

Number of copy number aberrations between segments

See Also

countingBreakPoints

Examples

cna(cnvData = maskCNV_BRCA)