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.
None published for Bioconductor
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
5,780
Files
113
Compiled share
55.9%
Has compiled src
Yes
Language breakdown
API
Exported functions
8
Internal functions
3
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.06
testthat edition
3
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
- Help pages
- 25 (1 internal)includes a package overview page
- Examples that run
- 100%8 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- cfTools-vignette HTML
Repository practices
Checks run against github.com/jasminezhoulab/cftools on 2026-10-21.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| CancerDetector.markers | data.frame | 1,266 × 3 | No other package |
| CancerDetector.reads | data.frame | 9,991 × 2 | No other package |
| CpG_OB_demo | data.frame | 2,224 × 5 | No other package |
| CpG_OT_demo | data.frame | 2,556 × 5 | No other package |
| beta_matrix | data.frame | 20 × 3 | No other package |
| cfDeconvolve.markers | data.frame | 10 × 8 | No other package |
| cfDeconvolve.reads | data.frame | 942 × 2 | No other package |
| cfsort_markers | data.frame | 51,035 × 4 | No other package |
| cfsort_reads | data.frame | 99,999 × 2 | No other package |
| demo.fragment_level.meth.bed | data.frame | 552 × 9 | No other package |
| demo.refo_frag.bed | data.frame | 559 × 6 | No other package |
| demo.refo_meth.bed | data.frame | 552 × 8 | No other package |
| demo.sorted.bed | data.frame | 1,117 × 6 | No other package |
| marker_index | data.frame | 3 × 1 | No other package |
| markers.bed | data.frame | 3 × 4 | No other package |
| sample_type | data.frame | 20 × 1 | No other package |
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 package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.