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).
enrichment(target, control, threshold, correction = "fdr")Set of goldi output for a target set of articles.
Set of goldi output for a control set of articles.
Only investigate associations which have been founder greater than this number of times.
Correction to impliment on association P values. Users may choose any value which p.adjust may accept.
A formated data.frame with three columns: terms, enrichments, and P values.
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 \(\frac{\frac{b}{n}}{\frac{B}{N}}\).
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<U+2013>7. http://doi.org/10.1186/1471-2105-10-48