Data

Data,InfoDataFrame-method

InfoDataFrame-method

[,InfoDataFrame,ANY,ANY,ANY-method

[,InfoDataFrame-method

colNames

colNames,InfoDataFrame-method

data.frame2InfoDataFrame

dim,InfoDataFrame-method

dimLabels

dimLabels,InfoDataFrame-method

ncol

ncol,InfoDataFrame-method

nrow

nrow,InfoDataFrame-method

rowNames

rowNames,InfoDataFrame-method

show,InfoDataFrame-method

an object of class <code>InfoDataFrame</code>

object

a logic for matrices and arrays. If TRUE the result is
coerced to the lowest possible dimension. This only works for
extracting elements, not for the replacement

drop


Methods defined for class <code>InfoDataFrame</code>.


methods

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.

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InfoDataFrame-method: Methods defined for S4 class InfoDataFrame

Description

Usage

Arguments

See Also