References

The following table lists the command line parameters for INRICH analysis. Options in bold* are requisite. When optional argument is a file, pay special attention to compile your input file adhering to the formatting requirements listed in the Format (4th) column. Also, note that all input file columns are tab-separated.

Option Option name Default value(s) Format Description
-2 test-type no designation -2 or no designation default : enrichment statistic is calculated based on the number of testing intervals overlapping with pathway genes
-2 : enrichment statistic is calculated based on the number of pathway genes overlapping with testing intervals
-a* test-interval-file   -a file-name

chr start_bp stop_bp 		List of associated genomic interval regions from GWAS analysis
-b background-gene-file   -b file-name

gene_id 		List of genes with special interest
Pathway analysis can be restricted to genes listed in this file. For example, users may be interested in analyzing a subset of reference genes that are expressed only in a specific tissue type.
-c pre-compute true -c

Turn off the precomputing option that searches acceptable positions for random interval generation prior to permutation
Precomputing speeds up the permutation procedure at the expense of increased memory usage. We thus suggest to turn off the precompute option (by specifying -c), when more than 1000 genomic intervals are examined or when memory allocation error messages appear.

-d match-density 0.2 -d numeric float

Allow (-d) % SNP mapping density extension for random intervals

-e match-genes true -e

If used, omit the random set generation criterion that matches the number of overlapping genes for each interval with the input interval set with the original test regions

-f random-seed 0 -f numeric integer Useful if want to repeat an analysis and get the same output
-g* reference-gene-file   -g file-name

chr start_bp stop_bp gene_id gene_name 		List of reference genes
-h positional clustering   -h top-N-closest-regions Conduct positional clustering test on top-N-closest regions
-i, -j target size-filter -i 2
-j 200 		-i numeric integer
-j numeric integer		 Restrict analysis to the gene sets with at least (-i) genes but not more than (-j) number of genes
-k compact true -k Turn off the compact option that excludes non-genic test intervals
-m* reference-SNP-file    -m file-name

chr bp 		List of reference SNPs included in the GWAS analysis
-n top-N-regions all -n numeric integer Restrict analysis to the top N intervals listed in the test input file
-o output-root inrich -o alphabet/numeric string

Output file name

-p display-p 0.05 -p numeric float Displays pathways significant below this threshold as part of the standard output and log file
-q num-bootstrapping 1000 -q numeric integer Number of permutations to carry out for correcting empirical pathway-level p-values
-r num-replicates 5000 -r numeric integer Number of permutations to carry out for calulating empirical pathway-level p-values
-t* geneset-file   -t file-name

gene_id gene_set_id gene_set_description 		List of gene and gene sets
-u human GWAS data true -u Designate that test data are from non-human genome
-w bp-window 0 -n numeric integer   Extend gene regions to include (-w) bp up/downstream
-x range-file   -x file-name

chr start_bp stop_bp 		List of genomic ranges with special interst
Pathway analysis can be restricted to a subset of reference genes based on their genomic location specified in this file.
-z min-obs threshold 2 -z numeric integer

Restrict analysis to the gene sets with at least -z number of genes overlapping with test intervals