safedag {safe}R Documentation

SAFE results displayed in Gene Ontology

Description

SAFE results are displayed on the directed acyclic graph for one of the ontologies under investigation. Category-wide significance displayed by node color.

Arguments

object Object of class SAFE
ontology Gene Ontology of interest. Character strings of "GO.CC", "GO.BP", and "GO.MF" accepted.
top Optional character string giving the node name from which to draw a subgraph of the tree
file Optional filename for a post-script of the graph
color.cutoffs Numeric vector of length 3 for the cutoffs for coloring significant nodes. Nodes with unadjusted p-values less than color.cutoff[3] are drawn in blue; less than color.cutoff[2] are drawn in green; less than color.cutoff[1] are drawn in red.
filter Optional integer (1,2,3) to only include branches that contain at least one node as significant as the respective color.cutoff.
max.GOnames Maximum size of DAG to include category names as labels.

Details

DAG-plots are suggested as a means for visualizing the extent of differential expression in Gene Ontology categories. The relatedness of significant categories suggests whether similar or disparate biological findings are identified.

Author(s)

William T. Barry: bill.barry@duke.edu

References

W. T. Barry, A. B. Nobel and F.A. Wright, 2005, Significance Analysis of functional categories in gene expression studies: a structured permutation approach, Bioinformatics {bf 21}(9) 1943–1949.

See also the vignette included with this package.

See Also

{safe.}


[Package safe version 2.2.0 Index]