GOGeneSets


a single character value specifying a choice of species: "Dm" ("Drosophila_
melanogaster"), "Hs" ("Homo_sapiens"), "Rn" ("Rattus_norvegicus"), "Mm"
("Mus_musculus") or "Ce" ("Caenorhabditis_elegans"))


species


a single character value or a character vector specifying an ontology or
multiple ontologies. The current version provides the following choices: 
"BP", "CC" and "MF"


ontologies


This function creates a list of gene sets based on GO terms. It is
species-specific, and returns a list of gene sets, each of which 
is a character vector of Entrez identifiers.


This package provides classes and methods for gene set
over-representation, enrichment and network analyses on
high-throughput screens. The over-representation analysis is
performed based on hypergeometric tests. The enrichment
analysis is based on the GSEA algorithm (Subramanian et al.
PNAS 2005). The network analysis identifies enriched
subnetworks based on algorithms from the BioNet package
(Beisser et al., Bioinformatics 2010). A pipeline is also
specifically designed for cellHTS2 object to perform
integrative network analyses of high-throughput RNA
interference screens. The users can build their own analysis
pipeline for their own data set based on this package.

Xin Wang

HTSanalyzeR

Gene set over-representation, enrichment and network analyses
for high-throughput screens

GOGeneSets function

a single character value specifying a choice of species: "Dm" ("Drosophila_
melanogaster"), "Hs" ("Homo_sapiens"), "Rn" ("Rattus_norvegicus"), "Mm"
("Mus_musculus") or "Ce" ("Caenorhabditis_elegans"))

a single character value or a character vector specifying an ontology or
multiple ontologies. The current version provides the following choices: 
"BP", "CC" and "MF"

This function creates a list of gene sets based on GO terms. It is
species-specific, and returns a list of gene sets, each of which 
is a character vector of Entrez identifiers.

GOGeneSets: Create a list of gene sets based on GO terms

Description

Usage

Arguments

Value

Details

See Also

Examples