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ctDNAtools

The ctDNAtools package provides functionalities to analyze circulating tumor DNA (ctDNA)/ cell-free DNA (cfDNA) sequencing data. The tools cover analysis of ctDNA/cfDNA fragmentation and analysis of cancer minimal residual disease.

Package overview

Installation

# From github

# install.packages("devtools")
devtools::install_github("alkodsi/ctDNAtools")

Getting started

Browse the vignette here

Citation

Alkodsi A, Meriranta L, Pasanen A, Leppä S (2020). “ctDNAtools: An R package to work with sequencing data of circulating tumor DNA.” bioRxiv.

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Version

Install

install.packages('ctDNAtools')

Monthly Downloads

8

Version

0.4.0

License

MIT + file LICENSE

Issues

5

Pull Requests

0

Stars

41

Forks

12

Maintainer

Amjad Alkodsi

Last Published

March 4th, 2020

Functions in ctDNAtools (0.4.0)

get_mutations_fragment_size

Gets reads fragment lengths for a list of mutations
mutations

Example mutations data to use with ctDNAtools package
extract_trinucleotide_context

Extracts the trinucleotide context for a set of mutations
merge_mutations_in_phase

Collapses mutations in phase into one event
filter_mutations

Filters a set of mutations
summarize_fragment_size

Summarizes fragment size in defined genomic regions
get_mutations_read_names

Gets names of the reads showing reference and alternative allele of a list of mutations
test_ctDNA

Tests the ctDNA positivity of a sample
get_read_counts

Gets read counts for a specific locus in the genome
targets

Example Genomic targets to use with ctDNAtools package
get_mutations_read_counts

Counts ref and alt reads for a set of mutations
get_bam_chr

Helper function to extract chromosome names from a bam file
vcf_to_mutations_df

Helper function to read a vcf into the required format of mutations data frame
analyze_fragmentation

Provides fragment ends analysis
get_hist_bins

Helper function to bin a variable
bin_fragment_size

Gets histogram of fragment lengths from a bam file
get_mutation_read_names

Gets names of the reads showing reference and alternative alleles of a mutation
positivity_test

Computes a p-value of ctDNA positivity with a Monte-Carlo based sampling test
simulator

A function to sample from binomial distribution
verify_tag

Helper function to verify a tag exists
compare_simulated_observed

Compares simulated and observed variant allele counts
create_background_panel

Creates a background panel from a list of bam files
get_background_rate

Computes the background mismatch rate from a bam file
get_bam_SM

Helper function to extract SM from a bam file
create_background_panel_instance

Creates a background panel instance from a bam file (e.g. healthy samples)
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)
get_fragment_size

Gets fragment lengths from a bam file