WKS Documentation

Description
Testing the significance of ranked gene-sets in genome-wide transcriptome profiling data using weighted Kolmogorov-Smirnov statistics developed by Konstantina Charmpi and Bernard Ycart.

Homepage
http://www.thua45.cn/grit-2.0

Release
Binary-1.0      Windows       01/12/2025    http://www.thua45.cn/grit-2.0/programs/wks/wks-1.0.zip

Install
Go the source folder and run "g++ *.cpp -std=c++11 -lpthread -o wks" command, a binary named "wks" will produced in the folder.
Under Windows OS try "g++ *.cpp -std=c++11 -static -lpthread -o wks.exe" instead.

Requirement
Minimum 8GB RAM, if you install from the source code, the g++ complier is also required.

Usage
wks-1.0 -s gene_set -l gene_list [-n simulation_n] [-t thread] [-o output]

Options
-s ranked gene-sets.
-l ranked gene-list.
-n number of simulations.
-t multithreading, default 1. Usually set to the number of CPU cores.
-o output, output file name.

Example Data
ranked gene-set: Pig10.2-WKS.gmt	http://www.thua45.cn/grit-2.0/programs/wks-1.0/Human-WKS.gmt
ranked gene-list: GSE45967_MYCN_gene-list.txt	http://www.thua45.cn/grit-2.0/programs/wks-1.0/GSE45967_MYCN_gene-list.txt

Example
An example run should like: wks-1.0 -s Human-WKS.gmt -i GSE45967_MYCN_gene-list.txt -t 8 -o output.txt.
This command takes two input files: Human-WKS.gmt and GSE45967_MYCN_gene-list.txt. It will produce an output file named output.txt. Full instruction is avaiavle in Flaver's user manual.

References
Charmpi K, Ycart B. Weighted Kolmogorov Smirnov testing: an alternative for Gene Set Enrichment Analysis. Stat Appl Genet Mol Biol. 2015 Jun;14(3):279-93. doi: 10.1515/sagmb-2014-0077. PMID: 26030794.

Contact
Dr. Tinghua Huang, thua45@126.com
Dr. Min Yao, minyao@yangtzeu.edu.cn