enrichment: Calculate enriched terms in a target set

Description Usage Arguments Details Value References

View source: R/enrichment.R

Description

Given a target set of articles under question, we wish to compare the frequencies of term occurance to a control set of articles. We set a threshold above which to investigate terms (setting this threshold higher reduces spurious associated but decreases power to identify true associations) and calculate the enrichment and the P value of association (see hgt for more details).

Usage

1
enrichment(target, control, threshold, correction = "fdr")

Arguments

target

Set of goldi output for a target set of articles.

control

Set of goldi output for a control set of articles.

threshold

Only investigate associations which have been founder greater than this number of times.

correction

Correction to impliment on association P values. Users may choose any value which p.adjust may accept.

Details

This function mimics a truncated version of the output of GOrilla by identifying and quantifying the enrichment of terms in a target set of articles. Given N articles and B associations of the given term, the enrichment of b terms in the n articles in the target set is given by \frac{\frac{b}{n}}{\frac{B}{N}}.

Value

A formated data.frame with three columns: terms, enrichments, and P values.

References

Eden, E., Navon, R., Steinfeld, I., Lipson, D., & Yakhini, Z. (2009). GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics, 10(1), 1<e2><80><93>7. http://doi.org/10.1186/1471-2105-10-48


Chris1221/GOldilocks documentation built on July 6, 2017, 6:31 a.m.