smooth_segments: Smooth simple clonal CNAs.

In caravagnalab/CNAqc: CNAqc - Copy Number Analysis quality check

Smooth simple clonal CNAs.

Description

This function joins simple clonal CNAs that have the same Major and minor alleles, and that are zeparate by at most a certain number of nucleotides. The pre-smoothing copy number segments are retained in the output computation.

Usage

smooth_segments(x, maximum_distance = 1e+06)

Arguments

x	A CNAqc object.
maximum_distance	The maximum number of nucleotides to join two equivalent segments.

Value

A CNAqc object with smoothed segments, which retains also the pre-smooting dataset.

Examples

data('example_dataset_CNAqc', package = 'CNAqc')
x = init(mutations = example_dataset_CNAqc$mutations, cna = example_dataset_CNAqc$cna, purity = example_dataset_CNAqc$purity)

# Before smoothing
print(x)
x = smooth_segments(x)

# After smoothing
plot_smoothing(x)

caravagnalab/CNAqc documentation built on Oct. 31, 2024, 3:54 a.m.