safe (version 3.12.0)

safedag: SAFE results displayed in Gene Ontology

Description

SAFE results are displayed in a directed acyclic graph for the Gene Ontology under investigation. Category-wide significance is displayed by node color.

Usage

safedag(object = NULL, ontology = NULL, top = NULL,  color.cutoffs = c(0.1, 0.01, 0.001), filter = 0,  max.GOnames = 200)

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 top category name from which to draw a subgraph of the tree

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.

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 21(9) 1943--1949.

See also the vignette included with this package.

See Also

safe.