load_input: Load data for TIN.

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

Description

The function can support both a file argument and a dataframe. In the case a file is given, no column or row names should be used. If the input is a dataframe or tibble, column names are required. See the package for a detailed description of the input format for TIN analysis.

This function, after loading data, annotates which mutation has VAF within a custom range (default [0; 0.7]); these are the only mutations that are used for the TIN analysis.

Usage

load_input(x, verbose = FALSE, VAF_range_tumour = c(0, 0.7),
  N = 20000)

Arguments

x	Either a filename, or a dataframe.
verbose	If 'TRUE', more output is print to screen.
VAF_range_tumour	A 2D vector that determines a VAF range used to decide which mutation we do analyse from the input cancer 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 list that contains the following informations: tumour calls, normal calls and joint calls, plus the input VAF range and file name.

Examples

# Generating a random TIN input
load_input(random_TIN())

caravagn/TIN documentation built on Dec. 10, 2019, 11:21 a.m.