TimeTP README

* Prerequisites for TimeTP
0) Python 2.X
1) R packages : Limma, Deseq2
2) Python modules : Numpy (1.6.2 <=), Scipy (0.15.0 <=), NetworkX

* To run TimeTP,
1) Make a GRN and PIN file for your species of interest.
   The path to files should be addressed in the configuration file.
2) Make a group file, a probe-gene file in the directory where your gene expression files (CEL or read count file) are.
   The path to data should be addressed in the configuration file.
3) Make a configuration file in the TimeTP directory.
4) Run as './TimeTP [name_of_config_file]'

* How to make a configuration file
Below is the sample configuration file (tab-delimited).
------------------------------------------------------------------------
type	RNA-seq
readType        single-read
dataDir 	/Path_to_Your_Dataset_Directory
outDir  	/Path_to_Your_Result_Directory
GRNFilePath     /Path_to_GRN_File/File_name
PINFilePath     /Path_to_PIN_File/File_name
species		hsa
downloadFiles	yes
KEGGGeneFilePath	/Path_to_KEGG_Gene_File/File_name
KEGGPathFilePath	/Path_to_KEGG_Pathway_File/File_name
xmlFilePath	/Path_to_xml_File_Directory
single		0
countFile    	count.txt
groupFile	group.txt
geneConvFile	gene_conv.txt
numTP   	10
threshold       0.05
maxDelay        1
removeT0        1
FDR     	1
k		20
------------------------------------------------------------------------
1) type 	: 'RNA-seq' OR 'Microarray'
2) readType 	: Only for RNA-seq data. 'single-read' OR 'paired-end'
3) dataDir 	: Path to the directory that includes your files (CEL or raw count).
4) outDir	: Path to the output directory that results will be saved.
5) GRNFilePath	: Path to GRN file. GRN file is a tab-delimited file with TF (first column) and target gene (second column) name.
		  TF and gene name can be an official gene symbol or Entrez ID.
6) PINFilePath	: Path to PIN file. PIN file is a tab-delimited file with gene (first column) and gene (second column) name.
		  Gene name can be an official gene symbol or Entrez ID.
7) species	: KEGG organism code with three characters. It can be found at http://www.kegg.jp/kegg/catalog/org_list.html
8) downloadFiles	: yes or no to download relevant files from KEGG, including a KEGG gene name file, a KEGG pathway list file and XML files for each pathway.
			  If you say 'no', you should provide the file paths in 9), 10) and 11).
			  If you say 'yes', the files will be downloaded in the /.../TimeTP/[species] folder.
9) KEGGGeneFilePath	: (Write only when you wrote 'no' in 8)
			  Path to KEGG-Gene symbol file. You can download it as http://rest.kegg.jp/list/[KEGG_organism_code]
10) KEGGPathFilePath	: (Write only when you wrote 'no' in 8)
			  Path to KEGG pathway list file. You can download it as http://rest.kegg.jp/list/pathway/[KEGG_organism_code]
11) xmlFilePath		: (Write only when you wrote 'no' in 8)
			  Path to a directory consisting of XML files from each KEGG pathway.
12) single	: '0' for Control-Treatment samples and '1' for single time-series samples.
13) countFile	: Only for RNA-seq data. Name of the raw read count input file.
		  This file should be comma-delimited, with column and row headers.
		  *** Column headers should be matched with sample names in the groupFile.***
		  The number of column headers should be same as the number of samples.
		  *** Row headers should be matched with probe names in the geneConvFile OR should be gene symbols.***
14) groupFile	: Name of the group file.
		  Group file consists of two columns (tab-delimited).
		  * First column - group number.
		  	i) Single time-series samples
				Samples for the first time point : 0
				Samples for the second time point : 1
				...
				Samples for the Nth time point : N-1
			ii) Control-treatment time-series samples
				Control samples for the first time point : 0
				Control samples for the second time point : 1
				...
				Control samples for the Nth time point : N-1
				Treatment samples for the first time point : N
				...
				Treatment samples for the Nth time point : 2N-1
		  * Second column - sample names.
			i) Microarray : same as CEL file names.
			i) RNA-seq    : same as column headers of countFile. 
15) geneConvFile: Name of the gene conversion file.
		  Gene conversion file consists of two columns (tab-delimited).
		  * First column - Probe name
		  * Second column - Gene symbol (Entrez ID or Official gene symbol)
		  If row headers in countFile are already gene symbols, geneConvFile can be 'NA'.
16) numTP	: The number of time points.
17) threshold	: Threshold for P-value (Default : 0.05)
18) maxDelay	: Maximum delay of expression propagation (Default : 1)
		  1 implies TimeTP allows expression propagation across one time point or less.
		  It depends on whether time interval between time-series samples are short or long.
19) removeT0	: '1' for removing DEGs found in the first time point and '0' for not removing them.
		  (Default : 0 for single time-series, 1 for control-treatment)
20) FDR		: '1' for using FDR corrected P-value for DEG selection and '0' for not using it. (Default : 1)
21) k		: The maximum number of TFs to find by influence maximization algorithm. (Default: 20)