Analyzing cell-free DNA methylation data with cfTools

cfTools is an R package for cell-free DNA (cfDNA) methylation data analysis, including (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.

Introduction

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.

Specifically, cfTools can deconvolve different sources of cfDNA fragments (or reads) in two contexts:

1. Cancer detection: separate cfDNA fragments into tumor-derived fragments and background normal fragments (2 classes), and estimate the tumor-derived cfDNA fraction $\theta$ ($0\leq \theta < 1$).

2. Tissue deconvolution: separate cfDNA fragments from different tissues (> 2 classes), and estimate the cfDNA fraction $\theta_t$ ($0\leq \theta_t < 1$) of different tissue types (including an unknown type) $t$ for a plasma cfDNA sample.

These functions can serve as foundations for more advanced cfDNA-based studies, including cancer diagnosis and disease monitoring.

Installation

cfTools is an R package available via the Bioconductor repository for packages. You can install the release version by using the following commands in your R session:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
BiocManager::install("cfTools")

Alternatively, you can install the development version from GitHub :

BiocManager::install("jasminezhoulab/cfTools")

Vignettes

See the detailed documentation for cfTools using the following commands in your R session

browseVignettes("cfTools")