fosterlab / CFTK

The co-fractionation toolkit

CFTK

CFTK is a toolkit for the analysis of co-fractionation mass spectrometry (CF-MS) data. It implements many common tasks for CF-MS data analysis, including preprocessing of CF-MS datasets, evaluating data quality, and inference of protein-protein interaction networks. To learn more about the package, download and open the "Introduction to CFTK" vignette at https://github.com/fosterlab/CFTK/tree/master/vignettes.

System requirements

CFTK relies on functions from the following R packages:

	dplyr (>= 0.7.4),
	tidyr (>= 1.1.2),
	readr (>= 1.3.1),
	purrr (>= 0.3.4),
	stringr (>= 1.4.0),
	magrittr (>= 1.5),
	arules (>= 1.6-1),
	gtools (>= 3.5.0),
	lsa (>= 0.73.1),
	pbapply (>= 1.3.4),
	propr (>= 3.1.8),
	treeClust (>= 1.1-7),
	vegan (>= 2.5-6),
	wccsom (>= 1.2.11),
	GENIE3 (>= 1.6.0),
	Pigengene (>= 1.12.0),
	WGCNA (>= 1.51),
	pcaPP (>= 1.9-73),
	AUC (>= 0.3.0),
	reshape2 (>= 1.4.3),
	naivebayes (>= 0.9.1),
	ranger (>= 0.8.0),
	LiblineaR (>= 2.10-8),
	speedglm (>= 0.3-2),
	tester (>= 0.1.7)

CFTK has been tested with R version 3.6.0 and higher.

Installation

To install CFTK, first install the devtools package, if it is not already installed:

> install.packages("devtools") 

Then, install the required dependencies from Bioconductor:

> if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
> BiocManager::install(c("AnnotationDbi", "GO.db", "preprocessCore", "impute", "Pigengene", "GENIE3"))

Also install the kohonen package, which is required by wccsom:

> install.packages("kohonen")

Next, the wccsom package, which is no longer distributed via CRAN, must be manually installed. To do so, download and extract the wccsom package from https://cran.r-project.org/src/contrib/Archive/wccsom/wccsom_1.2.11.tar.gz. For example, on Unix systems, this can be done using wget by entering the following commands into a terminal:

wget https://cran.r-project.org/src/contrib/Archive/wccsom/wccsom_1.2.11.tar.gz
tar -xzvf wccsom_1.2.11.tar.gz

Then, open R and install wccsom using devtools:

> devtools::install("wccsom")

On a Windows machine, installing wccsom is slightly more complicated. First, navigate to https://cran.r-project.org/src/contrib/Archive/wccsom/wccsom_1.2.11.tar.gz using a web browser in order to download the wccsom package. Then, download Rtools and follow the installation instructions. Last, from R, install wccsom by entering the following command, replacing the string MyUserName with your own username, or updating the path to the wccsom package as needed.

> install.packages("C:\\Users\\MyUserName\\Downloads\\wccsom_1.2.11.tar.gz", repos = NULL, type = "source")

Finally, install CFTK from GitHub using devtools:

> devtools::install_github("fosterlab/CFTK")

This should take no more than a few minutes.

Usage

For an in-depth guide to the functionality of CFTK, download the "Introduction to CFTK" vignette (file intro-to-CFTK.html) at https://github.com/fosterlab/CFTK/tree/master/vignettes, and open this HTML file in a web browser. The vignette demonstrates the application of CFTK to carry out several exemplary analyses in a published CF-MS dataset. This data is available from the data-raw directory (at https://github.com/fosterlab/CFTK/tree/master/data-raw).