countingBaseSegments: countingBaseSegments

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

countingBaseSegments

Description

Function for counting altered base segments

Usage

countingBaseSegments(
  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

Details

The Altered Base Segment calculation takes all the CNV data for a single patient and first filters it for a segmentation mean of > 0.2 and, if specified, the minimum number of probes covering that area. Then, it calculates the sums of the lengths of each segment for a particular patient and outputs that.

Number\ of\ Altered\ Bases = \sum^{R}_{i = 1} d_i\ where\ |\bar{y}_{S_i}| \ge 0.2

Value

Number of Base segments for each unique sample

Examples

countingBaseSegments(cnvData = maskCNV_BRCA)

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