patternGOanalysis: patternGOanalysis

Description

Performs GO analysis on genes for each pattern

Usage

patternGOanalysis(pattern, type = NULL, termnum = 20, identifier = "ENSEMBL", species = "Human")

Arguments

pattern

The direct output of truetimepattern or pseudotimepattern function.

type

Character value of specific pattern to perform the GO analysis. If NULL GO analysis will be performed for all patterns.

termnum

Number of top GO terms to be displayed.

identifier

The identifier of the genes. It should be one of the following: "Entrez", "GenBank", "Alias", "Ensembl", "Gene", "Symbol", "GeneName" and "UniGene"

species

The species of the genes. Currently only "Human" and "Mouse" are supported

Value

A list where each element is a data.frame containing the results of GO analysis.

Details

This function is basically a wrap up of functions in the topGO package. It takes as input the output of truetimepattern or pseudotimepattern function. For each pattern, the GO enrichment analysis is performed where input genes are genes with specific patterns and background genes are all genes in the expression profile. Users should correctly select identifier and species, otherwise the function may breakdown.

Examples

Run this code

library(topGO)
data(HSMMdata)
pattern <- truetimepattern(HSMMdata,truetime,removeconstant=TRUE)
patternGOanalysis(pattern,termnum=20,identifier="ENSEMBL",species="Human")