Flaver Documentation

Description

Testing the significance of ranked gene-sets in genome-wide transcriptome profiling data using weighted rank correlation statistics

Release

Source code 1.0.3 08/18/2024

Source code 1.0.2 07/31/2023

Source code 1.0.1 08/31/2022

Source code 1.0.0 06/14/2022

Binary Windows, Mac OS, Linux

Install

Go the source folder and run g++ main.cpp -std=c++11 -lpthread -o flaver command, a binary named flaver will produced in the folder.

Under windows OS try g++ main.cpp -std=c++11 -static -lpthread -o flaver.exe instead.

Requirement

Minimum 2GB memory, if you install from the source code, the g++ complier is also required.

Usage

flaver -s gene_set -i gene_list [-g tscore] [-r adjust] [-w weight] [-p auto_p] [-t thread] [-o output] [-d outdata]

Options

-s ranked gene-sets.

-i ranked gene-list.

-g gene-set score, less than this value will be omitted in the analysis, default 10.

-r two letter parameter for data adjust (first letter for gene-set, second letter for gene-list), 1 for as is, 2 for absolute value, and 3 for reverse value (x * -1.0), default "11". Example of "12" will be take the gene-set value as is and the absolute values for gene-list.

-w weighting method, 1 by geometric mean of gene-set and gene-list, 2 by gene-list, 3 by gene-set, 4 by geometric mean of gene-set and gene-list (ori), 5 by gene-list (ori), 6 by gene-set (ori), 7 by mixed-density, 8 by gene-list-density, 9 by gene-set-density, default 1.

-p auto p, default is off.

-t multithreading, default 1. Usually set to the number of CPU cores.

-o output, output file name.

-d output data file name.

Example Data

Supplemental data file: supplemental_data2.zip

Example

An example run should like: ./flaver -s grit-human-v100-j20-2.bed -i duodenum_gapsig-e6.txt -g 1.3 -w 3 -t 8 -o duodenum_ output.txt

This command took two input files: grit-human-v100-j20-2.bed, duodenum_gapsig-e6.txt. After finished run it will produce an output file nameded duodenum_ output.txt.

External Links

Jinzer web site: http://www.thua45.cn/jinzer

References

Min Yao, Hao He, Binyu Wang, Xinmiao Huang, Sunli Zheng, Jianwu Wang, Xuejun Gao, Tinghua Huang. Testing the significance of ranked gene-sets in genome-wide transcriptome profiling data using weighted rank correlation statistics.

Contact

Dr. Tinghua Huang, thua45@126.com

Dr. Min Yao, minyao@yangtzeu.edu.cn