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Extract Absolute Copy-Number Features

ExtractCopyNumberFeatures.Rd

Extract genome-wide copy-number features data from either a list of dataframes or a QDNAseq S4 object for 1 or more samples. This function is intended to be run on absolute CN data.

Usage

ExtractCopyNumberFeatures(
  CN_data,
  genome,
  cores = 1,
  log_features = FALSE,
  extra_features = FALSE
)

Arguments

CN_data

List of dataframes or S4 QDNAseq object. Segmented copy-number data for for 1 or more samples. If input is a list of dataframes, columns should be:

  1. chromosome

  2. start

  3. end

  4. segVal

genome

Character string. The reference genome used for alignment.
Options: 'hg19', 'hg38'

cores

Integer. The number of cores to use for parallel processing.

log_features

FALSE or char vector. If a vector of feature names is provided, take the log1p of these extracted CN-features.

extra_features

Logical. If TRUE, extracts CN-feature data for two more features: nc50, and cdist.

Value

A list. Each list element contains feature data for a single feature.

Details

The extracted copy-number features are:

  1. Breakpoint count per 10MB - bp10MB

  2. Copy-number value of each segment - copynumber

  3. Copy-number difference between adjacent segments - changepoint

  4. Breakpoint count per chromosome arm - bpchrarm

  5. Lengths of oscillating CN segment chains - osCN

  6. Size of copy-number segments in base-pairs - segsize

Extra features:
7. Minimum number of chromosomes (a count) needed to account for 50% of CN changes in a sample - nc50
8. Distance in base pairs of each breakpoint to the centromere - cdist