README.md

# TriPOINT
A pathway analysis tool that integrates non-coding regulators for further gene prioritization.

**User Manual**: https://github.uconn.edu/raw/ajt06004/TriPOINT/master/UserManual.pdf

**Binary file**: https://github.uconn.edu/ajt06004/TriPOINT/raw/master/tripoint.jar *Note: RServe will need to be installed and started in R.  See the User Manual for a guide to set this up.*

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

**-prox**	Sets the proximity based non-coding target threshold which spans the base pair distance both upstream and downstream from the transcription start site.  Default: 50000