README.md

In allenaigit/pathwayko: PathwayKO: An R package for knock-out pathway enrichment analysis

PathwayKO

PathwayKO: An R package for knock-out pathway enrichment analysis

PathwayKO is an R package for knock-out pathway enrichment analysis, excavating the true positive KO KEGG pathways that contain and are impacted by a KO gene at the system-level. It enables ROC curve-based statistics analysis for assessing the performance of methods in terms of AUC (area under ROC curve), partial AUCs, Youden's best p-value threshold, specificity, sensitivity, accuracy, precision and recall. It is flexible to incorporate custom methods and currently integrates the state-of-the-art SPIA, ROntoTools (PE and pDIS), PADOG, GSA, GESA and SAFE. A benchmark dataset of mouse 10 KO GEO datasets is embedded for demo. The PathwayKO package provides a novel solution to the knock-out pathway enrichment analysis.

Installation

This is an R package. So you should first have R installed on your OS. (here's how).

To install this package from source code (and in this case, source code from Github), devtools should be installed once R is in place. Also, you need to have BiocManager installed so that all R package dependencies are kept consistent under BioConductor. PathwayKO was built under R version 4.0.2 and BioConductor version 3.11, older versions of R and BioConductor may still work but were not tested.

Afterwards having installed R and BioConductor, launch your R session, and use the following commands to install PathwayKO ("pathwayko" is the package name identifier used in R):

library(devtools)
# If installing from Github
devtools::install_github("allenaigit/pathwayko") 

If there is any missing dependencies, you will be prompted during installation and your installation may fail. Just update/install any missing packages following the prompt then try again. You may need more than one try to take care of all dependencies.

Note: under *nix systems, default path for R package installation is "/usr/local/lib/R" which usually requires root access to write into it. Alternatively you can install packages under your home directory (e.g. "\~/R/"), which makes such packages only available to you and not other users.

Usage

library(pathwayko)
preprocess()
pathwayko()

Note: more details for usages are available in pathwayko/inst/docs/Users_manual.pdf

Issue

All issues and/or suggestions should be directed to Issues page, and please be sure to attach sufficient descriptions and materials to reproduce any issue you may encounter.

License

CC BY-NC-ND 4.0

allenaigit/pathwayko documentation built on Nov. 23, 2022, 5:43 p.m.