safedag: SAFE results displayed in Gene Ontology
In safe: Significance Analysis of Function and Expression

Description Usage Arguments Details Author(s) References See Also

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

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

`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.

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.

William T. Barry: bbarry@jimmy.harvard.edu

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.

safe.

safe documentation built on Nov. 8, 2020, 5:37 p.m.