# TINC - Tumour-in-Normal contamination assessment

## Documentation for package ‘TINC’ version 0.1.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

autofit | Runs a TINC analysis.
check_CHIP_variants | Check for CHIP variants in normal and tumour at high VAF
fit_example | Example TINC fit
load_TINC_input | Load TINC input data.
load_VCF_Canvas | Canvas VCF parsing function
load_VCF_Canvas_Manta | Merged Canvas and Manta VCF parsing function
load_VCF_CNA_DRAGEN | DRAGEN VCF CNA parsing function
load_VCF_smallVar_DRAGEN | DRAGEN VCF small variants parsing function
load_VCF_Strelka | Strelka 2 VCF parsing function
plot.tin_obj | Plot a TINC analysis.
plot_full_page_report | Plot a full page detailed report of the TINC analysis
plot_simple_report | Plot a strip short report of the TINC analysis.
print.tin_obj | Print a TINC object to screen
random_TIN | Generate a random dataset for TINC.
to_string | Dataframe description of a TINC fit