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README
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Download link:
http://omics.fudan.edu.cn/static/softwares/
README for LEGO (V2.0)
Time-stamp: <2015-10-13 12:00 by Xinran Dong & Yun Hao & Zhu Liu>
* INTRODUCTION
----------------------------------------------------------------------
We have developed a novel method named LEGO (functional Link Enrichment of Gene Ontology or gene sets). Incorporating a network-based gene-weighting scheme, LEGO measures the overlaps between the interesting genes and a given gene set by integrating both the gene weights and gene-gene interactions.
Please Cite:
LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights.
* HOWTO COMPILE THE SOURCE AND INSTALL
----------------------------------------------------------------------
You will need a Unix environment with a working C++ compiler to
compile the source files in src/. We recommend GCC>=4.2.
Besides, Perl and R are necessary for running this program.
Type
$ perl compile.pl
This will create a binary directory ( /bin) in the main directory.
* USAGE
----------------------------------------------------------------------
In the main directory, you could type:
$ perl LEGO.pl
and you will see the help message.
The usage for this program:
###############################################################################################
perl LEGO.pl <network file> <geneset file> <interest file> [options]
Options:
-h/-help: show help message.
-pre: <whether or not to pre-run to generate mid files,1-yes,0-no(e.g:0)>
-multi: <multi or not:1-yes,0-no(e.g:0)>
-bgNE: <bgNE for the network,e.g:0.25>
-min: <minimum gene set size,e.g:5>
-max: <maximum gene set size,e.g:10000>
-adj: <adjusted methods,e.g:fdr>
-p_thre: <p value cutoff,e.g:0.05>
-fisher: <whether or not run fisher exact test, 1-yes,0-no,e.g: 0>
-filter: <whether or not run result cluster and filter step, 1-yes, 0-no, e.g: 1>
-bg_file: <background file, e.g: bg.txt, if do not have background file, leave it blank>
###############################################################################################
And we also provide a version that do not use permutation strategy:
The usage for this program:
###############################################################################################
perl LEGO_noperm.pl <network file> <geneset file> <interest file> [options]
Options:
-h/-help: show help message.
-pre: <whether or not to pre-run to generate mid files,1-yes,0-no(e.g:0)>
-multi: <multi or not:1-yes,0-no(e.g:0)>
-bgNE: <bgNE for the network,e.g:0.25>
-min: <minimum gene set size,e.g:5>
-max: <maximum gene set size,e.g:10000>
-adj: <adjusted methods,e.g:fdr>
-p_thre: <p value cutoff,e.g:0.05>
-fisher: <whether or not run fisher exact test, 1-yes,0-no,e.g: 0>
-filter: <whether or not run result cluster and filter step, 1-yes, 0-no, e.g: 0>
-bg_file: <background file, e.g: bg.txt, if do not have background file, leave it blank> \n";
###############################################################################################
Example1 (for single interesting gene list file):
perl LEGO.pl demo/FC2_human.txt demo/GeneSet_human.txt demo/input.txt
Example2 (for multiple interesting gene list file):
perl LEGO.pl demo/FC2_human.txt demo/GeneSet_human.txt demo/input_mul.txt -multi 1
Example3 (for single interesting gene list file and filtered results):
perl LEGO.pl demo/FC2_human.txt demo/GeneSet_human.txt demo/input.txt -filter 1
Example4 (for multiple interesting gene list file and filtered results):
perl LEGO.pl demo/FC2_human.txt demo/GeneSet_human.txt demo/input_mul.txt -multi 1 -filter 1
Example5 (for single interesting gene list file + bg file):
perl LEGO.pl demo/FC2_human.txt demo/GeneSet_human.txt demo/input.txt -bg_file demo/bg.txt
Example6 (for single interesting gene list file with background list):
perl LEGO_noperm.pl demo/FC2_human.txt demo/GeneSet_human.txt demo/input.txt -bg_file demo/bg.txt
Example7 (for multiple interesting gene list file with background list):
perl LEGO_noperm.pl demo/FC2_human.txt demo/GeneSet_human.txt demo/input_mul.txt -multi 1 -bg_file demo/bg.txt
Tips:
1. Output files: <interest file>_LEGO.txt, if you choose to filter & cluster enriched gene sets, another two files will be generated: <interest file>_LEGO_filter.txt <interest file>_LEGO_filter_cluster.txt (set -filter 1)
2. The first time to run this program will take about several minutes to generate mid-files(according to the size of the network and genesets). If you want to re-generate the mid files, set `-pre_run to 1`;
If you have already generated the mid-files for network and genesets, it will only take several seconds to calculate a new input gene list (set `-pre_run to generate mid files` to 0)
3. The first time to use LEGO.pl, it will take maybe several minutes to generate the permutation results. We provide the pre-generated mid files for data/GeneSet_human.txt.
4. If you want to use the background file, you could only use LEGO_noperm.pl;
5. The gene ID in the network, gene set and input gene list must be the same ID system.
6. More options are available at our online server <http://lego.tianlab.cn>. It will be available soon.
## for plot
Pre-request:
Usage: plot_LEGO.R <input interesting gene list file> <enriched output file> <output file prefix> <network file name> <network+gene set prefix,e.g: demo/GeneSet_human.txt_FC2_human> <CS or NW> <plot gene set name, can be comma saperated>
## e.g:
Rscript src/plot_LEGO.R demo/input.txt demo/input.txt_id.out_LEGO.txt demo/input_REACTOME_KINESINS demo/FC2_human.txt demo/GeneSet_human.txt_FC2_human CS REACTOME_KINESINS