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Bin and Smooth Copy Number Data from Coverage File

Source: R/CNVplot.R
CovBin.Rd

Splits the coverage data by chromosome, bins into 300bp windows, and computes smoothed copy number values using a larger window size.

Usage

CovBin(cov, cov_binsize)

Arguments

cov

Data frame or tibble. Must include columns CONTIG, START, END, and CNF.

cov_binsize

Numeric. Bin size (in bases) for smoothing (e.g., 10000 for 10kb).

Value

A data frame with columns: CONTIG, bin_start, bin_norm_id, and smoothed CNF values.

Details

  • Bins are generated every 300bp within each region.

  • Smoothed copy number is computed as the median CNF within each larger (cov_binsize) window.

Examples

# CovBin(cov, cov_binsize = 10000)