windowGOanalysis: windowGOanalysis

In SEPA: SEPA

Description

Performs GO analysis with moving window for transition patterns

Usage

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 <[e-mail]>

Examples

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

SEPA documentation built on May 6, 2019, 2:42 a.m.