subset_by_minimum_CCF: Subset mutations by minimum CCF

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

Subset mutations by minimum CCF

Description

Retains only a subset of mutations, if they have CCF above a cutoff. Note that subclonal CNAs are lost upon application of this function.

Usage

subset_by_minimum_CCF(x, min_target_CCF = 0.1)

Arguments

x	A new CNAqc object with subset data.
min_target_CCF	The minimum CCF do be enforced.

Examples

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

# Original data
plot_data_histogram(x)

# Original data if CCF is above 10%
plot_data_histogram(subset_by_minimum_CCF(x))

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