CINmetrics: CINmetrics

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

CINmetrics

Description

Calculate all CINmetrics on a given dataframe

Usage

CINmetrics(
  cnvData,
  sample_column = 1,
  segmentMean_tai = 0.2,
  segmentMean_cna = (log(1.7, 2) - 1),
  segmentMean_base_segments = 0.2,
  segmentMean_break_points = 0.2,
  segmentMean_fga = 0.2,
  numProbes = NA,
  segmentDistance_cna = 0.2,
  minSegSize_cna = 10,
  genomeSize_fga = 2873203431
)

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_tai	numerical value for the minimum segment_mean cutoff/ threshold for Total Aberration Index calculation. Default is 0.2
segmentMean_cna	numerical value for the minimum segment_mean cutoff/ threshold for Copy Number Aberration calculation. Default is 0.2
segmentMean_base_segments	numerical value for the minimum segment_mean cutoff/ threshold for Base segments calculation. Default is 0.2
segmentMean_break_points	numerical value for the minimum segment_mean cutoff/ threshold for Break points calculation. Default is 0.2
segmentMean_fga	numerical value for the minimum segment_mean cutoff/ threshold for Fraction of genome altered calculation. Default is 0.2
numProbes	Number of Probes
segmentDistance_cna	Segment distance threshold
minSegSize_cna	Minimum segment size
genomeSize_fga	Size of the genome derived from Affymetrix 6.0 array probe. Default is 2873203431 calculated based on hg38 **excluding sex chromosomes**

Value

All Chromosomal INstability metrics

Examples

CINmetrics(cnvData = maskCNV_BRCA)

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