callCNV: Call Copy Number Variation Using QDNAseq Utilities

In hw538/cfDNAPro: cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA

Call Copy Number Variation Using QDNAseq Utilities

Description

This function leverages QDNAseq to process BAM files for CNV analysis. It applies a sequence of operations including binning, filtering, correcting, normalizing, smoothing, segmenting, and calling to generate a QDNAseqCopyNumbers object.

Usage

callCNV(bamfile, bin_size = 1000, genome_label = "hg19")

Arguments

bamfile	A string specifying the path to a single BAM file.
bin_size	A numerical value indicating the size of the bins (default is 1000).
genome_label	A string specifying the genome label (default is "hg19").

Value

A 'QDNAseqCopyNumbers' object containing the copy number variation results.

Examples

callCNV(bamfile = "path/to/your/file.bam", bin_size = 1000, genome_label = "hg19")

hw538/cfDNAPro documentation built on Feb. 17, 2025, 6:09 p.m.