Liquid Biopsy Cell-Free DNA Fragment Analyser — cfDNAPro documentation (original) (raw)

cfDNAPro logo

Welcome to the documentation for cfDNAPro. Use the menu on the left to explore more about the tool. Below is a brief overview:

Brief Introduction

cfDNAPro is a bioinformatics R package designed for the curation and analysis of cfDNA fragment features, which play a crucial role in the early detection of cancer and ongoing disease monitoring. This package facilitates the extraction of key biological features from cfDNA Next-Generation Sequencing (NGS) data, including fragment size, fragment end motif, copy number (CN), and mutations. Analyzing and visualizing these features typically involves using multiple tools, which can be time-consuming.

To streamline this process, cfDNAPro provides two primary sets of functions: one for data characterization and another for data visualization.

A Quick Example

cfDNAPro can be installed in R by following these instructions (additional details):

if (!require(devtools)) install.packages("devtools") library(devtools) devtools::install_github("hw538/cfDNAPro", build_vignettes = TRUE)

To visualise the fragment size mode of each sample,cfDNAPro can read pre-existing insert size metrics files from multiple cohort sub-folders stored in_path/to/main/folder_:

library(cfDNAPro) path <- "path/to/main/folder" myplot <- callMode(path = path) %>% plotMode()

Currently cfDNAPro is compatible exclusively with insert sizes metrics files produced by Picard Tools, using the CollectInsertSizeMetrics tool, which can be accessed here. Future versions will include additional features.

R Package Vignettes

To access the vignettes in RStudio (you have to indicatebuild_vignettes = TRUE during the aforementioned installation step), use the command:

browseVignettes("cfDNAPro")

Citation

If you use cfDNAPro in any published work, please cite:

Haichao Wang, Paulius D. Mennea et al (2020). cfDNAPro:An R/Bioconductor package to extract and visualise cell-free DNA biological features. R package version 1.7 https://github.com/hw538/cfDNAPro

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