safedag {safe} | R Documentation |
SAFE results are displayed on the directed acyclic graph for one of the ontologies under investigation. Category-wide significance displayed by node color.
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. |
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: bill.barry@duke.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 {bf 21}(9) 1943–1949.
See also the vignette included with this package.
{safe
.}