Function reference • ctDNAtools

Minimal Residual Disease testing
`test_ctDNA()`	Tests the ctDNA positivity of a sample
`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)
`merge_mutations_in_phase()`	Collapses mutations in phase into one event
`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
`get_background_rate()`	Computes the background mismatch rate from a bam file
`filter_mutations()`	Filters a set of mutations
Fragmentation
`get_fragment_size()`	Gets fragment lengths from a bam file
`bin_fragment_size()`	Gets histogram of fragment lengths from a bam file
`summarize_fragment_size()`	Summarizes fragment size in defined genomic regions
`analyze_fragmentation()`	Provides fragment ends analysis
`get_mutations_fragment_size()`	Gets reads fragment lengths for a list of mutations
Other
`extract_trinucleotide_context()`	Extracts the trinucleotide context for a set of mutations
`vcf_to_mutations_df()`	Helper function to read a vcf into the required format of mutations data frame
Data
`mutations`	Example mutations data to use with ctDNAtools package
`targets`	Example Genomic targets to use with ctDNAtools package

Reference