domainEnrichment: Domain enrichment in a desired system.
In hyginn/BCB420.2019.ESA: Exploratory Systems Analysis Tools

Description Usage Arguments Details Value Details Author(s) See Also Examples

domainEnrichment Find the enriched domains in selected system and interpret enrichment by plot.

1	domainEnrichment(system, alpha = 0.05)

`system`	The shortehand notation of selected system, five-letter code as discussed in class.
`alpha`	The alpha value for Benjamini-Hochberg control. Default is 0.05.

For the PHYLA system, see details in the PHALY domain enrichemnt vignette (or load the vignette with vignette("domainEnrichment-Vignette", package = "BCB420.2019.ESA")).

A data frame that include domains in the system with its counts and frequency in system and in random genes; p-value, odd ratio, adjust p-value and enrichment; interpro descriptions. Return NULL if system is not available by SyDBgetSysSymbols.

This function is created as part of BCB420 2019 winter course. The domain databaase were fetched from InterPro, see more details in fetchData.

Fan Shen (aut)

fetchData Fetch data from package

SyDBgetRootSysIDs Get the system ID in database

SyDBgetSysSymbols Get the genes in desired system

## Not run: 
# Plot enrichend domains in PHALY system orderd by rich factor
# Plot would separate to two parts if too many domains are enriched
# User can hover around the point on plot to get more info (i.e ID descripton)
system <- "PHALY"
domainEnrichment(system)

## End(Not run)