load_TINC_input: Load TINC input data.

In caravagn/TINC: TINC - Tumour-in-Normal contamination assessment

Load TINC input data.

Description

The function loads input mutations and optional copy number data for TINC. Input formats are reported at the package website.

After loading data, mutation with VAF outside a range (default [0; 0.7]) are removed from analysis. Similarly, mutations are down-sampled if in excess of some threshold (default 'N=20000').

Usage

load_TINC_input(x, cna, VAF_range_tumour = c(0, 0.7), N = 20000)

Arguments

x	A dataframe or tibble with input mutation data, reporting 'chr', 'from', 'to', 'ref' and 'alt', plus 'n_ref_count' and 'n_alt_count', and 't_ref_count' and 't_tot_count'.
cna	Copy Number data in the format of package CNAqc, providing 'chr', 'from', 'to', 'Major' and 'minor'.
VAF_range_tumour	VAF range used to filter mutations from the tumour sample.
N	If there are more than 'N' mutations in VAF range 'VAF_range_tumour', a random subset of size 'N' is retained.

Value

A tibble with the loaded data.

Examples

# Generating a random TIN input
rt = random_TIN()
load_TINC_input(x = rt$data, cna = rt$cna)

caravagn/TINC documentation built on April 28, 2024, 7:42 a.m.