Description Usage Arguments Details Value References

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).

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

`target` |
Set of |

`control` |
Set of |

`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 |

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}}*.

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

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.

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