selectGO-methods: selectGO method generics

In ShadowFiendSF/GSminer: Select gold standard including positive and negative genes pairs based on the Gene Ontology

Description

selectGO method generics

select the GO term based on the threshold

Usage

## S4 method for signature 'GSminer'
selectGO(object, u = 0.5, l = 0.25,
  method = c("Resnik", "Lin", "Schlicker", "Jiang", "Pesquita"),
  multicores = NULL, seed = NA)

Arguments

object	the GSminer object
u	the upper bound, 1/2 by default
l	the lower bound, 1/4 by default
method	method for computing the similarity
multicores	an integer to specify how many cores will be registered as the multicore parallel backend to the 'foreach' package.
seed	for reproducibility, the seed of the random number generator can be set to a fixed value before adding noise.

Value

a vector which name is selected GO term

Author(s)

Li Zhaohong && Wu Zefeng

Examples

inputFile <- paste0(system.file(package = "GSminer"), "/extdata/TAIR.GO")
miner <- GSminer(inputFile = inputFile, sep = "\t")
#just for an example
#selectGO(miner,u = 0.5, l = 0.25, method= "Resnik", multicores = 2)

ShadowFiendSF/GSminer documentation built on May 29, 2019, 3:03 p.m.