dcFunArgs

an input function name (character string)

logical to indicate whether the function will act as it
should be (with assigned values in the current environment). By
default, it sets to FALSE

action

logical to indicate whether the messages will be
displayed in the screen. By default, it sets to TRUE for display

verbose


<code>dcFunArgs</code> is supposed to assign (and evaluate) arguments with
default values for an input function.


There lacks a package for analysing domain-centric ontologies and annotations, particularly those in the dcGO database. The dcGO (http://supfam.org/SUPERFAMILY/dcGO) is a comprehensive domain-centric database for annotating protein domains using a panel of ontologies including Gene Ontology. With the package, users are expected to analyse and visualise domain-centric ontologies and annotations. Supported analyses include but are not limited to: easy access to a wide range of ontologies and their domain-centric annotations; able to build customised ontologies and annotations; domain-based enrichment analysis and visualisation; construction of a domain (semantic similarity) network according to ontology annotations; significance analysis for estimating a contact (statistical significance) network via Random Walk with Restart; and high-performance parallel computing. The new functionalities are: 1) to create domain-centric ontologies; 2) to predict ontology terms for input protein sequences (precisely domain content in the form of architectures) plus to assess the predictions; 3) to reconstruct ancestral discrete characters using maximum likelihood/parsimony.

dcFunArgs: Function to assign (and evaluate) arguments with default values for an input function

Description

Usage

Arguments

Value

See Also

Examples