From 36ea8cef039f88d274b987b8204394f6830a67b3 Mon Sep 17 00:00:00 2001 From: ajt06004 Date: Wed, 24 Jan 2018 02:14:40 -0500 Subject: [PATCH] README corrections. --- README.md | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index 2aa0a4b..ad938ec 100644 --- a/README.md +++ b/README.md @@ -1,38 +1,38 @@ # TriPOINT A pathway analysis tool that integrates non-coding regulators for further gene prioritization. -Binary file: tripoint.jar +**Binary** file: tripoint.jar Available datasets are in the data directory. -Usage: java -jar tripoint.jar -db -o +**Usage:** java -jar tripoint.jar -db -o #Parameters --db Sets pathway database to import pathways from GRAPHITE. Values available: "kegg", "reactome", "biocarta", "humancyc", "nci", "panther" +**-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 +**-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) +**-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 +**-up** Sets the up-regulated gene threshold. Default: 0.05 --down Sets the down-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 +**-w** Sets the weak activation/inhibition factor. Default: 0.5 --p Controls the impact of gene expression when calculating measures. Default: 0.25 +**-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 +**-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 +**-perm** Sets the number of permutations for p-value calculations. Default: 10000 --rstate Sets the random state for reproducible results. Default: Current Time (milliseconds) +**-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. +**-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 +**-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 +**-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 +**-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