network propagation based method(NP-method)
Developed by Ting Wang, 2013.12.13
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Contact:
	Ting Wang: wang9ting@gmail.com
	Jin Gu: wellgoo@gmail.com
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System requirement:
	Linux/Unix OS, Windows OS,
	installed R,
	> 8G memory.
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R scripts:
should be execute one bye one
(1) precalculate_M.R
	to precalculate and prestore M matrix for NP-method, skip if using the default M matrix.
(2) NP.fg.R
	to get foreground NPES.
(3) NP.bg.R
	to get background NPES distributions using gene set permutation analysis, to save time users can execute parallelly, but please pay attention to the file directions.
(4) NP.pvalue.R
	to normalize NPES and get p-value using the outputs of NP.fg.R and NP.bg.R.
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Input files:
(1) A_adjmat_htri.Rdata
	a adjacent matrix for the HTRI network
(2) M_htri_rwr0.5.Rdata
	a N*N matrix, named p.single, which is precalculated as the M matrix of NP-method using precalculate.R (with parameters HTRI network and r=0.5).
(3) TS6.2_hsa.miRFam.mat.txt
	a matrix representing the TargetScan v6.2 annotated conserved targets of miRNA families, each column is a geneset, 0/1 represents geneset containing the gene or not;
(4) DE_test.GSE4107.txt
	gene differential expression file, 2 columns, first is gene name, second is score.
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Output files:
(1) output of precalculate_M.R
	M matrix file: containing a matrix variable named p.single.
(2) outputs of NP.fg.R
	NPES.txt: foreground NPES and size information
	LE.txt: leading-edge (LE) targets
	genelist.net.txt: intermediate file, expressions of genes in networks
	geneset.net.txt: intermediate file, genesets containing the genes in networks
	gene_p.single.txt: intermediate file, sorted network genes according to single seed based RWR in the farward searching procedure
	score_rank.txt: intermediate file, sorted targets, fold change and NPES scores of each miRNA target set, every 3 lines are these information of one miRNA target set
(3) outputs of NP.bg.R
	NPES.bg.txt: background NPES
(4)	output of NP.pvalue.R
	NPES_result.txt: results of the NPES score, normalized score, p-value and FDR for each miRNA
note: some NA values in some outputs are reasonable (including the warnings during runing R), because not all genes in network have expression measurements.