print.biopax: Print a biopax object.

In rBiopaxParser: Parses BioPax files and represents them in R

Description

Print a biopax object.

Usage

## S3 method for class 'biopax'
print(x, ...)

Arguments

x	A biopax object to print.
...	Other arguments to be passed to print.

Examples

 data(biopaxexample)
 print(biopax) 

Example output

Loading required package: data.table
Summary of the biopax object:
            Length Class                             Mode     
namespaces  5      SimplifiedXMLNamespaceDefinitions character
ns_rdf      1      -none-                            character
ns_owl      1      -none-                            character
ns_bp       1      -none-                            character
file        1      -none-                            character
biopaxlevel 1      -none-                            numeric  
dt          6      biopax_df                         list     

Internal data:
$namespaces
                                               rdf 
     "http://www.w3.org/1999/02/22-rdf-syntax-ns#" 
                                                bp 
"http://www.biopax.org/release/biopax-level2.owl#" 
                                              rdfs 
           "http://www.w3.org/2000/01/rdf-schema#" 
                                               owl 
                  "http://www.w3.org/2002/07/owl#" 
                                               xsd 
               "http://www.w3.org/2001/XMLSchema#" 
attr(,"class")
[1] "SimplifiedXMLNamespaceDefinitions" "XMLNamespaceDefinitions"          

$ns_rdf
[1] "rdf"

$ns_owl
[1] "owl"

$ns_bp
[1] "bp"

$file
[1] "docu/vignette/exampledata.owl"

$biopaxlevel
[1] 2

$dt
                         class                 id          property
  1:                 bioSource       Homo_sapiens              NAME
  2:                 bioSource       Homo_sapiens        TAXON-XREF
  3:           unificationXref NCBI_taxonomy_9606                DB
  4:           unificationXref NCBI_taxonomy_9606                ID
  5:                dataSource example_DataSource              NAME
 ---                                                               
919: physicalEntityParticipant     ex_x_101435_30 CELLULAR-LOCATION
920:       sequenceParticipant   ex_x_101860_5907   PHYSICAL-ENTITY
921:       sequenceParticipant   ex_x_101860_5907 CELLULAR-LOCATION
922:       sequenceParticipant   ex_x_101441_5569   PHYSICAL-ENTITY
923:       sequenceParticipant   ex_x_101441_5569 CELLULAR-LOCATION
     property_attr                     property_attr_value       property_value
  1:  rdf:datatype http://www.w3.org/2001/XMLSchema#string         Homo sapiens
  2:  rdf:resource                     #NCBI_taxonomy_9606                     
  3:  rdf:datatype http://www.w3.org/2001/XMLSchema#string        NCBI_taxonomy
  4:  rdf:datatype http://www.w3.org/2001/XMLSchema#string                 9606
  5:  rdf:datatype http://www.w3.org/2001/XMLSchema#string example biopax model
 ---                                                                           
919:  rdf:resource                          #transmembrane                     
920:  rdf:resource                            #ex_m_101860                     
921:  rdf:resource                              #cytoplasm                     
922:  rdf:resource                            #ex_m_101441                     
923:  rdf:resource                                #nucleus                     

Dimension of internal data.table:  923,6 

Summary of parsed internal data.table 
    class                id              property         property_attr     
 Length:923         Length:923         Length:923         Length:923        
 Class :character   Class :character   Class :character   Class :character  
 Mode  :character   Mode  :character   Mode  :character   Mode  :character  
 property_attr_value property_value    
 Length:923          Length:923        
 Class :character    Class :character  
 Mode  :character    Mode  :character  

rBiopaxParser documentation built on Nov. 8, 2020, 8:21 p.m.