dcSupraBetter: Function to find supra-domains with better scores than their...
In dcGOR: Analysis of Ontologies and Protein Domain Annotations

Description Usage Arguments Value Note See Also Examples

dcSupraBetter is supposed to find supra-domains with better scores than their individual domains.

1	dcSupraBetter(input.file, output.file = NULL, verbose = T)

`input.file`	an input file used to build the object. This input file contains original annotations between domains/features and ontology terms, along with the hypergeometric scores (hscore) in support for their annotations. For example, a file containing original annotations between SCOP domain architectures and GO terms can be found in http://dcgor.r-forge.r-project.org/data/Feature/Feature2GO.sf.txt. As seen in this example, the input file must contain the header (in the first row) and three columns: 1st column for 'Feature_id' (here SCOP domain architectures), 2nd column for 'Term_id' (GO terms), and 3rd column for 'Score' (hscore)
`output.file`	an output file containing results. If not NULL, a tab-delimited text file will be also written out, with 1st column 'Feature_id' for features/domains, 2nd column 'Term_id' for ontology terms, 3rd column 'Score' for hypergeometric scores (indicative of strength for feature-term associations). Otherwise, there is no output file (by default)
`verbose`	logical to indicate whether the messages will be displayed in the screen. By default, it sets to TRUE for display

a data frame containing three columns: 1st column 'Feature_id' for features, 2nd 'Term_id' for terms, and 3rd 'Score' for the hypergeometric score indicative of strength of associations beteen features and terms

When 'output.file' is specified, a tab-delimited text file is output, with the column names: 1st column 'Feature_id' for features, 2nd 'Term_id' for terms, and 3rd 'Score' for the hypergeometric score indicative of strength of associations beteen features and terms

dcList2Matrix

## Not run: 
input.file <-
"http://dcgor.r-forge.r-project.org/data/Feature/Feature2GO.sf.txt"
res <- dcSupraBetter(input.file)
res[1:10,]

## End(Not run)