hdfisher.go: Hypothesis-Driven Fisher Test

In ptm: Analyses of Protein Post-Translational Modifications

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')

ptm documentation built on Aug. 7, 2022, 5:05 p.m.