Description

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

Usage

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

Arguments

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

Value

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

Note

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

Examples

input.file <-
"http://dcgor.r-forge.r-project.org/data/Feature/Feature2GO.sf.txt"
res <- dcSupraBetter(input.file)

Reading the file 'http://dcgor.r-forge.r-project.org/data/Feature/Feature2GO.sf.txt' ...
There are 7263 supra-domains and 1446 individual domains.
A total of 123999 annotations (for 5655 supra-domains) have better scores.
res[1:10,]

      Feature_id      Term_id      Score  
 [1,] "100895,100895" "GO:0035374" "25.05"
 [2,] "100895,100895" "GO:0033691" "15.42"
 [3,] "100895,100895" "GO:0043395" "17.46"
 [4,] "100895,100895" "GO:1901681" "13.58"
 [5,] "100895,100895" "GO:0031406" "4.28" 
 [6,] "100895,100895" "GO:0030545" "31.77"
 [7,] "100895,100895" "GO:0030234" "17.29"
 [8,] "100895,100895" "GO:0043168" "1.84" 
 [9,] "100895,100895" "GO:0001948" "19.23"
[10,] "100895,100895" "GO:0032403" "8.32" 

Source code

Source man

See also