Man pages for ctDNAtools
Analyze Circulating Tumor DNA Sequencing Data

analyze_fragmentationProvides fragment ends analysis
bin_fragment_sizeGets histogram of fragment lengths from a bam file
compare_simulated_observedCompares simulated and observed variant allele counts
create_background_panelCreates a background panel from a list of bam files
create_background_panel_instanceCreates a background panel instance from a bam file (e.g....
create_black_listCreates a black list of genomic loci based on a background...
extract_trinucleotide_contextExtracts the trinucleotide context for a set of mutations
filter_mutationsFilters a set of mutations
get_background_rateComputes the background mismatch rate from a bam file
get_bam_chrHelper function to extract chromosome names from a bam file
get_bam_SMHelper function to extract SM from a bam file
get_fragment_sizeGets fragment lengths from a bam file
get_hist_binsHelper function to bin a variable
get_mutation_read_namesGets names of the reads showing reference and alternative...
get_mutations_fragment_sizeGets reads fragment lengths for a list of mutations
get_mutations_read_countsCounts ref and alt reads for a set of mutations
get_mutations_read_namesGets names of the reads showing reference and alternative...
get_read_countsGets read counts for a specific locus in the genome
merge_mutations_in_phaseCollapses mutations in phase into one event
mutationsExample mutations data to use with ctDNAtools package
positivity_testComputes a p-value of ctDNA positivity with a Monte-Carlo...
simulatorA function to sample from binomial distribution
summarize_fragment_sizeSummarizes fragment size in defined genomic regions
targetsExample Genomic targets to use with ctDNAtools package
test_ctDNATests the ctDNA positivity of a sample
vcf_to_mutations_dfHelper function to read a vcf into the required format of...
verify_tagHelper function to verify a tag exists
ctDNAtools documentation built on March 26, 2020, 7:39 p.m.