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 |