Description
dcBuildAnno is supposed to build an object of of the S4 class
Anno, given input files. These input files include 1) a
file containing domain information, 2) a file containing term
information, and 3) a file containing associations between domains and
terms.
Usage
dcBuildAnno(domain_info.file, term_info.file, association.file, output.file = "Anno.RData")
Arguments
- domain_info.file
- an input file containing domain information.
For example, a file containing InterPro domains (InterPro) can be found
in http://dcgor.r-forge.r-project.org/data/InterPro/InterPro.txt.
As seen in this example, the input file must contain the header (in the
first row), and entries in the first column intend to be domain ID (and
must be unique). Note: the file should use the tab delimiter as the
field separator between columns
- term_info.file
- an input file containing term information. For
example, a file containing Gene Ontology (GO) terms can be found in
http://dcgor.r-forge.r-project.org/data/InterPro/GO.txt. As seen
in this example, the input file must contain the header (in the first
row) and four columns: 1st column for term ID (must be unique), 2nd
column for term name, 3rd column for term namespace, and 4th column for
term distance. These four columns must be provided, but the content for
the last column can be arbitrary (if it is hard to prepare). Note: the
file should use the tab delimiter as the field separator between
columns
- association.file
- an input file containing associations between
domains and terms. For example, a file containing associations between
InterPro domains and GO Molecular Function (GOMF) terms can be found in
http://dcgor.r-forge.r-project.org/data/InterPro/Domain2GOMF.txt.
As seen in this example, the input file must contain the header (in the
first row) and two columns: 1st column for domain ID (corresponding to
the first column in 'domain_info.file'), 2nd column for term ID
(corresponding to the first column in 'term_info.file'). If there are
additional columns, these columns will be ignored. Note: the file
should use the tab delimiter as the field separator between columns
- output.file
- an output file used to save the built object as an
RData-formatted file. If NULL, this file will be saved into
"Anno.RData" in the current working local directory
Value
Any use-specified variable that is given on the right side of the
assigement sign '<-', which contains the built Anno object.
Also, an RData file specified in "output.file" is saved in the local
directory.
Note
If there are no use-specified variable that is given on the right side
of the assigement sign '<-', then no object will be loaded onto the
working environment.
Examples
# build an "Anno" object that contains SCOP domain superfamilies (sf) annotated by GOBP terms
InterPro2GOMF <-
dcBuildAnno(domain_info.file="http://dcgor.r-forge.r-project.org/data/InterPro/InterPro.txt",
term_info.file="http://dcgor.r-forge.r-project.org/data/InterPro/GO.txt",
association.file="http://dcgor.r-forge.r-project.org/data/InterPro/Domain2GOMF.txt",
output.file="InterPro2GOMF.RData")
An object of S4 class 'Anno' has been built and saved into '/Users/hfang/Sites/SUPERFAMILY/dcGO/dcGOR/InterPro2GOMF.RData'.
InterPro2GOMF
An object of S4 class 'Anno'
@annoData: 8899 domains, 2219 terms
@termData (InfoDataFrame)
termNames: GO:0001071 GO:0003824 GO:0004872 ... GO:0015467 GO:0072345
(2219 total)
tvarLabels: ID Name Namespace Distance
@domainData (InfoDataFrame)
domainNames: IPR000003 IPR000006 IPR000008 ... IPR029784 IPR029785
(8899 total)
dvarLabels: id level description