# Analyze Circulating Tumor DNA Sequencing Data

## Documentation for package ‘ctDNAtools’ version 0.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

analyze_fragmentation | Provides fragment ends analysis
bin_fragment_size | Gets histogram of fragment lengths from a bam file
create_background_panel | Creates a background panel from a list of bam files
create_black_list | Creates a black list of genomic loci based on a background panel created from a list of bam files (e.g. healthy samples)
extract_trinucleotide_context | Extracts the trinucleotide context for a set of mutations
filter_mutations | Filters a set of mutations
get_background_rate | Computes the background mismatch rate from a bam file
get_fragment_size | Gets fragment lengths from a bam file
get_mutations_fragment_size | Gets reads fragment lengths for a list of mutations
get_mutations_read_counts | Counts ref and alt reads for a set of mutations
get_mutations_read_names | Gets names of the reads showing reference and alternative allele of a list of mutations
merge_mutations_in_phase | Collapses mutations in phase into one event
mutations | Example mutations data to use with ctDNAtools package
summarize_fragment_size | Summarizes fragment size in defined genomic regions
targets | Example Genomic targets to use with ctDNAtools package
test_ctDNA | Tests the ctDNA positivity of a sample
vcf_to_mutations_df | Helper function to read a vcf into the required format of mutations data frame