Fixed errors with finding non-coding regulators by proximity.

Included datasets, binary file, and cytoscape xml file.

README.md

@@ -1 +1,38 @@
-# TriPOINT
+# TriPOINT
+A pathway analysis tool that integrates non-coding regulators for further gene prioritization.
+
+Binary file: tripoint.jar
+
+Available datasets are in the data directory.
+
+Usage: java -jar tripoint.jar <expression file> -db <pathway database> -o <output directory>
+
+#Parameters
+
+-db	Sets pathway database to import pathways from GRAPHITE.  Values available: "kegg", "reactome", "biocarta", "humancyc", "nci", "panther"
+
+-o	Sets output directory for saving result files.  REQUIRED
+
+-gid	Sets the conversion method for gene identifiers.  Refer to 'convertIdentifiers' in GRAPHITE. Default: "SYMBOL" (Currently other identifiers are not recommended)
+
+-up	Sets the up-regulated gene threshold.  Default: 0.05
+
+-down	Sets the down-regulated gene threshold.  Default: -0.05
+
+-w	Sets the weak activation/inhibition factor.  Default: 0.5
+
+-p	Controls the impact of gene expression when calculating measures.  Default: 0.25
+
+-r	Controls the rate of exponential decay to control edge distance in impact score calculation.  Default: 0.25
+
+-perm	Sets the number of permutations for p-value calculations.  Default: 10000
+
+-rstate	Sets the random state for reproducible results.  Default: Current Time (milliseconds)
+
+-refflat	Specifies the UCSC refflat file to use to identify TSS locations of genes in pathways. Required for identifying non-coding regulators. Gene identifiers will need to match those provided in the expression file.
+
+-ci	Sets the tab-delimited file for chromatin interaction data to identify non-coding targets of genes
+
+-nct	Sets the bed file for non-coding targets to be associated with genes. If chromatin interactions are provided these sites will be connected via chromatin interactions, otherwise it will be proximity based
+
+-proxSets the proximity based non-coding target threshold which spans the base pair distance both upstream and downstream from the transcription start site.  Default: 50000