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GOFilter

Filters gene lists based on Gene Ontology annotations. Only genes that are annotated with given GO terms are selected for output. This component takes the parent-child relationships of GO into account: a gene is annotated with a given GO term if it has annotation entries either for the exact GO term or some child term.

You may use GOSearch if you are interested in the actual mapping between the query terms and the matches or if you want to avoid R and Bioconductor.

Version 1.2
Bundle microarray
Categories Filter GO
Authors Kristian Ovaska (kristian.ovaska@helsinki.fi), Marko Laakso (Marko.Laakso@Helsinki.FI)
Issue tracker View/Report issues
Requires R ; AnnotationDbi (R-bioconductor) ; GO.db (R-bioconductor)
Source files component.xml GOFilter.r
Usage Example with default values

Inputs

Name Type Mandatory Description
bioAnnotation AnnotationTable Mandatory Annotations that are used as the basis for filtering.
in SetList Optional List of genes of interest. Genes of the annotation file are used if this input is missing.

Outputs

Name Type Description
out SetList Filtered gene sets.

Parameters

Name Type Default Description
geneColumn string "" Name of the gene ID column or an empty string referring to the first ID column of the table.
goColumn string "GO" Name of the GO annotation column
numMatches int 1 Required number of matching terms for the gene to be selected for output. This must be between 1 and n, where n is the number of terms. If numMatches is 1, a gene must be annotated with at least one GO term mentioned in 'terms'. If numMatches in n, a gene must be annotated with all GO terms.
setID string "%s_GOMatch" Name of the result sets. The pattern %s is expanded to the name of each set in question.
terms string (no default) Comma-separated list of GO terms that are used for filtering.

Test cases

Test case Parameters IN
bioAnnotation
IN
in
OUT
out
case1_num_matches_1 properties bioAnnotation in out

terms=GO:0050896,GO:0032501,GO:0016020,GO:0005488,GO:0060089

case2_num_matches_2 properties bioAnnotation in out

terms=GO:0050896,GO:0032501,GO:0016020,GO:0005488,GO:0060089,
numMatches=2

case3_num_matches_3 properties bioAnnotation in out

terms=GO:0050896,GO:0032501,GO:0016020,GO:0005488,GO:0060089,
numMatches=3

case4_num_matches_4 properties bioAnnotation in out

terms=GO:0050896,GO:0032501,GO:0016020,GO:0005488,GO:0060089,
numMatches=4

case5_no_groups properties bioAnnotation (missing) out

terms=GO:0050896,GO:0032501,GO:0016020,GO:0005488,GO:0060089,
numMatches=2,
geneColumn=.GeneName


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