windowGOanalysis {SEPA} | R Documentation |
Performs GO analysis with moving window for transition patterns
windowGOanalysis(pattern, type = "constant_up", windowsize = NULL, movesize = NULL, termnum = 20, identifier = "ENSEMBL", species = "Human")
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 |
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).
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.
Zhicheng Ji, Hongkai Ji <zji4@zji4.edu>
library(topGO) data(HSMMdata) pattern <- pseudotimepattern(HSMMdata,pseudotime) windowGOanalysis(pattern,type="constant_up")