countingBreakPoints: countingBreakPoints

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

countingBreakPoints

Description

The Break Point calculation takes all the CNV data for a single patient and first filters it for segmentation mean of > 0.2 and, if specified, the minimum number of probes covering that area. Then it counts the number of rows of data and multiplies it by 2. This represents the break points at the 5' and 3' ends of each segment.

Number\ of \ Break\ Points = \sum^{R}_{i = 1} (n_i \cdot 2)\ where\ |\bar{y}_{S_i}| \ge 0.2

Usage

countingBreakPoints(
  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

Value

Number of Break points for each unique sample

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