knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
library(TINC)

TINC is a package to estimate Tumour-in-Normal (TIN) and Tumour-in-Tumour (TIT) scores for a matched tumour-normal assay (ideally, a whole-genome one).

Input formats

TINC takes as input mutation data, with read counts reported for both the tumour and the matched normal.

Somatic mutations. Input mutations should report the following information:

Example input mutations are shown below.

Copy number segments. Optionally, allele-specific copy number segments can also be used These can be extremely important if the sample has high levels of aneuploidy, and we do suggest to use those in such cases.

Copy number segments data must follow the formats from the CNAqc package:

# devtools::install_github("caravagnalab/CNAqc")
require(CNAqc)

# This is the format
CNAqc::example_dataset_CNAqc$cna %>% print


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