enrichment: Calculate enriched terms in a target set
In goldi: Gene Ontology Label Discernment and Identification
Description
Usage
Arguments
Details
Value
References
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
goldi documentation built on May 2, 2019, 3:43 a.m.
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Description Usage Arguments Details Value References
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 |
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 |
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
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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