windowGOanalysis

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Description

Performs GO analysis with moving window for transition patterns

Usage

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windowGOanalysis(pattern, type = "constant_up", windowsize = NULL,
  movesize = NULL, termnum = 20, identifier = "ENSEMBL",
  species = "Human")

Arguments

pattern

The direct output of pseudotimepattern function.

type

The type of transition pattern.

windowsize

The number of genes in each group.

movesize

How many genes to move forward each time.

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

Details

This function is specifically designed for GO analysis of genes with a specific transition pattern. GO analyses are performed iteratively on a group of genes with similar transition points. Users can define the windowsize (the number of genes in each group) and the movesize (how many genes to move forward each time).

Value

A list where each element is a data.frame containing the results of GO analysis. The name of the list specifies the group of genes.

Author(s)

Zhicheng Ji, Hongkai Ji <zji4@zji4.edu>

Examples

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library(topGO)
data(HSMMdata)
pattern <- pseudotimepattern(HSMMdata,pseudotime)
windowGOanalysis(pattern,type="constant_up")