cfTools
Bioc currentInformatics Tools for Cell-Free DNA Study
Release Lineage
Entered 3.17 · Apr 26, 2023
Current · Requires R 4.6
Description
The cfTools R package provides methods for cell-free DNA (cfDNA) methylation data analysis to facilitate cfDNA-based studies. Given the methylation sequencing data of a cfDNA sample, for each cancer marker or tissue marker, we deconvolve the tumor-derived or tissue-specific reads from all reads falling in the marker region. Our read-based deconvolution algorithm exploits the pervasiveness of DNA methylation for signal enhancement, therefore can sensitively identify a trace amount of tumor-specific or tissue-specific cfDNA in plasma. cfTools provides functions for (1) cancer detection: sensitively detect tumor-derived cfDNA and estimate the tumor-derived cfDNA fraction (tumor burden); (2) tissue deconvolution: infer the tissue type composition and the cfDNA fraction of multiple tissue types for a plasma cfDNA sample. These functions can serve as foundations for more advanced cfDNA-based studies, including cancer diagnosis and disease monitoring.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
94 8 exported
Complexity
2.4 avg / 7 max
Call network
94 nodes / 47 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
5,782
Files
115
Compiled share
55.9%
Has compiled src
Yes
Language breakdown
API
Exported functions
8
Internal functions
3
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.06
testthat edition
3
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
14.3%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
file LICENSE
License flags
SPDX valid, not OSI
History
Versions
7
First release
2023-04-25
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
4
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Ran Hu author maintainer
- Shuo Li author
- Wenyuan Li author
- Mary Louisa Stackpole author
- Xianghong Jasmine Zhou author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("cfTools")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.