R: Gene set testing of gene set databases using Global Test
gt gene set testing methods
R Documentation
Gene set testing of gene set databases using Global Test
Description
A collection of procedures for performing the Global Test on gene set databases. Three function are provided for KEGG, for Gene Ontology and for the Broad Institute's gene sets.
The response variable of the regression model. This is passed on to the response argument of gt.
exprs
The expression measurements. May be
ExpressionSet or
matrix. Passed on to the alternative argument of
gt.
...
Any other arguments are also passed on to gt.
id
The identifier(s) of gene sets to be tested (character vector). If omitted, tests all gene sets in the database.
annotation
The name of the probe annotation package for the microarray that was used, or the name of the genome wide annotation package for the species (e.g. org.Hs.eg.db for human). If an organism package is given, the argument probe2entrez must be supplied. If annotation is missing, the function will attempt to retrieve the annotation information from the exprs argument.
probe2entrez
Use only if no probe annotation package is available. A mapping from probe identifiers to entrez gene ids. May be an environment, named list or named vector.
multtest
The method of multiple testing correction. Choose from: Benjamini and Hochberg FDR control (BH); Benjamini and Yekutieli FDR control (BY) or Holm familywise error fontrol (Holm). For gtGO also the focus level method is available. See focusLevel.
sort
If TRUE, sorts the results to increasing p-values.
ontology
The ontology or ontologies to be used. Default is to use all three ontologies.
minsize
The minimum number of probes that may be annotated to a gene set. Gene sets with fewer annotated probes are discarded.
maxsize
The maximum number of probes that may be annotated to a gene set. Gene sets with more annotated probes are discarded.
focuslevel
The focus level to be used for the focus level method. Either a vector of gene set ids, or a numerical level. In the latter case, findFocus is called with maxsize at the specified level to find a focus level.
collection
The Broad gene set collection, created by a call to getBroadSets.
conceptmatrix
The name of the file containing the importance weights, i.e. concept profile associations between Anni concepts. In the matrix contained in the file, columns correspond to testable concepts, and rows correspond to entrez-concepts. Useable files can be downloaded from http://biosemantics.org/index.php/software/weighted-global-test.
The relevance threshold for importance weights. Importance weights below the threshold are treated as zero.
share
If TRUE, the function divides the importance weight of a gene over all probes corresponding to the same entrez identifier. If FALSE, all probes get the full importance weight of the gene.
category
The subcategory of the Broad collection to be tested. The default is to test all sets.
Details
These are utility functions to make it easier to do gene set testing of gene sets available in gene set databases. The functions automatically retrieve the gene sets, preprocess and select them, perform global test, do multiple testing correction, and sort the results on the basis of their p-values.
All functions require that annotate and the appropriate annotation packages are installed. gtKEGG additionally requires the KEGG.db package; gtGO requires the GO.db package; gtBroad requires the user to download the XML file "msigdb_v2.5.xml"
from http://www.broad.mit.edu/gsea/downloads.jsp, and to preprocess that file using the getBroadSets function. gtConcept requires files that can be downloaded from http://biosemantics.org/index.php/software/weighted-global-test.
Goeman, Van de Geer, De Kort and Van Houwelingen (2004). A global test for groups of genes: testing association with a clinical outcome. Bioinformatics 20 (1) 93-99.
Goeman, Oosting, Cleton-Jansen, Anninga and Van Houwelingen (2005). Testing association of a pathway with survival using gene expression data. Bioinformatics 21 (9) 1950-1957.
See Also
The gt function. The gt.object and useful functions associated with that object.