MotifList-class: MotifList

In MotifDb: An Annotated Collection of Protein-DNA Binding Sequence Motifs

Description

A direct subclass of SimpleList, having no extra slots, in which listData is a list of position frequency matrices (PFMs), and the elementMetadata slot is a DataFrame with fifteen columns describing each matrix. Upon loading the MotifDb class, one MotifList object is instantiated and filled with matrices and their metadata. There should be no need for users to explicitly create objects of this class. When you load the MotifDb package, a fully-populated instance of this class is created, with > 2000 matrices with metadata

Methods

subset(x): extract matrices by metadata.

export(x): write matrices

show(x): describe matrices compactly

query(x): find matrices

Author(s)

Paul Shannon

Examples

    # Examine the number of matrices contributed by each source.
  print (table (values (MotifDb)$dataSource))

MotifDb documentation built on Nov. 8, 2020, 6:28 p.m.