knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
library(TINC)
TINC is a package to estimate Tumour-in-Normal (TIN) and Tumour-in-Tumour (TIT) scores for a matched tumour-normal assay (ideally, a whole-genome one).
TINC takes as input mutation data, with read counts reported for both the tumour and the matched normal.
Somatic mutations. Input mutations should report the following information:
chr
, from
, to
, ref
and alt
n_ref_count
and n_alt_count
. t_ref_count
and t_tot_count
. Example input mutations are shown below.
Copy number segments. Optionally, allele-specific copy number segments can also be used These can be extremely important if the sample has high levels of aneuploidy, and we do suggest to use those in such cases.
Copy number segments data must follow the formats from the CNAqc package:
chr
, from
and to
Major
and minor
alleles# devtools::install_github("caravagnalab/CNAqc") require(CNAqc) # This is the format CNAqc::example_dataset_CNAqc$cna %>% print
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