CINmetrics (version 0.1.0)

CINmetrics: CINmetrics

Description

Calculate all CINmetrics on a given dataframe

Usage

CINmetrics(
  cnvData,
  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

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

# NOT RUN {
CINmetrics(cnvData = maskCNV_BRCA)
# }