README

## perl script for gene function enrichment analysis (Fisher's Exact Test) ##
## Created by SherryDong (xrdong10@qq.com) ##
## Requirement: Linux, Perl, R ##
## USAGE:
	        enrich.pl  (v1.1)

                Usage:  enrich.pl  <database file> <input_file_name> <output_file_name>  [options]

				database file :  database file for enrichment analyais

				input_file_name:   input file name

				output_file_name:       output file name

				Options:

				-h  Show help

				-item   (item column number,default = 1)

                -des    (des column number, default = 2)

                -des_file (files to save description for genesets)

                -bg     (bacground_file_name,default=no background file)

                -list   (1-y|2-n,default=n)

                -thre   (threshold,default = 0.01)

                -max    (maximun size for des, default = no limitation)

                -min    (minmun size for des, default = no limitation)

                -adj    (need adj p value or not ,0-no,1-BH,2-FDR,default = no)

                -low    (low existence for match,default = 0)

                -multi  (whether the input has multi groups, default=0)

                -filter ( use what filter or not, default = 0 (do not use))

                -filter_column (filter column)
## Demo:
 perl enrich.pl  demo/omim/omim_disease_gene.txt demo/input.txt demo/output.txt -item 2 -des 1 -thre 0.1 -adj 2 -list 1