hdfisher.go {ptm} | R Documentation |
Hypothesis-Driven Fisher Test
Description
Carries out an enrichment Fisher's test using a hypothesis driven approach.
Usage
hdfisher.go(target, background, query, analysis = 'enrichment')
Arguments
target |
either a vector containing the UniProt IDs of the target set or the path to the txt file containing the list of IDs. |
background |
a dataframe with two columns (Uniprot ID and GO terms) and as many rows as different proteins there are in the background set. |
query |
character string defining the query. |
analysis |
a character string indicating whether the desired analysis is the enrichment ('enrichment') or depletion ('depletion'). |
Value
Returns a list that contains the contingency table and the p-Value.
Author(s)
Juan Carlos Aledo
References
Rhee et al. (2008) Nature Reviews Genetics 9:509–515.
See Also
search.go(), term.go(), get.go(), bg.go(), go.enrich(), gorilla(), net.go()
Examples
## Not run: hdfisher.go(c('Q14667', 'Q5JSZ5'), bg.go(c('Q14667', 'Q5JSZ5', 'P13196')), 'ion')
[Package ptm version 0.2.7 Index]