prepareGOannotation {goCluster} | R Documentation |
This function builds an association table between a given list of genes and their corresponding gene ontology annotations.
prepareGOannotation(uniqueID, annBuilderPkg, ontologies = ONTOLOGIES, evidence = EVIDENCECODES, trueID = NULL)
uniqueID |
The unique ID that should be associated with the gene ontology annotation. |
annBuilderPkg |
The AnnBuilder package that provides the basis for retrieving the annotation information. |
ontologies |
The ontologies that should be used. This has to be a character vector that contains one or more of the strings "MF", "BP", and/or "CC". |
evidence |
This character vector should contain the abbreviations for acceptable evidence codes. Please see the variable EVIDENCECODES for possible choices. The complete vector with all evidence codes is the default for the function. |
trueID |
The true ID specifies the type of ID that the gene
ontology information has been linked to (e.g. Locus Link). If this
ID differs from the the type of uniqueID this has to be
specified so that the IDs are converted accordingly. The option
needs to match the name of the AnnBuilder package environment
(without the prefix) that provides the conversion information. |
The gene ontology is organized as a hierarchical tree of terms with a parent-child relationship. By associating a gene with a term of this ontology the gene is implicitely linked with all parents of the term. In order to render the annotation of two gene lists comparable it is important to take this relationship into account.
The prepareGOannotation
function assembles a complete list of
gene <-> ontology associations based on the gene ontology
annotation. Duplicate genes are removed from the resulting table. This
removal should be based on the identifiers the gene ontology
information is linked to (e.g. Lokus Link) and it is possible to
specify this central ID by setting the trueid
option.
A composite list of the (possibly converted) unique ID and the association table.
annotations |
The association table linking the genes with gene ontology terms. Each gene can be linked to multiple GO entries and vice versa. |
uniqueid |
Either a copy of the original unique identifiers or a converted copy that matches the original vector in length but specifies the new gene ID for each gene. |
Gunnar Wrobel, http://www.gunnarwrobel.de.
prepareGOannotation(c("YGL213C", "YGL215W", "YGL216W", "YGL218W", "YGL219C", "YGL220W", "YGL221C", "YGL222C", "YGL223C", "YGL224C", "YGL225W"), "YEAST")