outputPosNeg-methods: outputPosNeg method generics

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

Description

outputPosNeg method generics

Output negative gene pairs

Usage

## S4 method for signature 'GSminer'
outputPosNeg(object, u = 0.5, l = 0.25,
  method.term = c("Resnik", "Lin", "Schlicker", "Jiang", "Pesquita"),
  method.gene = c("BM.average", "BM.max", "BM.complete", "average", "max"),
  multicores = NULL, verbose = TRUE, seed = NA,
  posFilename = "positiveGene.txt", negFilename = "negativeGene.txt",
  sep = "\t", filterByCC = TRUE, FNegFile = "negativeGene.filtered.txt")

Arguments

object	the GSminer object
u	the upper bound, 1/2 by default
l	the lower bound, 1/4 by default
method.term	method for computing the similarity
method.gene	the method used for how to derive semantic similarity between genes from semantic similarity between terms.
multicores	an integer to specify how many cores will be registered as the multicore parallel backend to the 'foreach' package.
verbose	logical to indicate whether the messages will be displayed in the screen.
seed	for reproducibility, the seed of the random number generator can be set to a fixed value before adding noise.
posFilename	postive gene output file name
negFilename	negative gene output file name without filtered by CC GO terms
sep	the delimiter of the file
filterByCC	weather filtered by CC GO terms by default is TRUE
FNegFile	negative gene output file name filtered by CC GO terms

Value

a vector which name is selected GO term

Author(s)

Lizhaohong && Wu Zefeng

Examples

inputFile <- paste0(system.file(package = "GSminer"), "/extdata/TAIR.GO")
miner <- GSminer(inputFile = inputFile, sep = "\t")
#outputPosNeg(miner, u = 0.1, l = 0.2, method.term = "Resnik", 
#             method.gene = "BM.average", multicores = 2, 
#             verbose = FALSE, posFilename = "pos.txt", 
#            filterByCC = FALSE, FNegFile = "neg.text")

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