subset: subset

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

subset

Description

An analog of the base package subset method, this version will return all the matrices whose metadata match the (possibly intricate) logical expression in the "subset" argument.

Note: just as with the base subset method, this method is unreliable except when used interactively. Batch, script or other programmatic use of this function is to be avoided.

Usage

## S4 method for signature 'MotifList'
subset(x, subset, select, drop=FALSE, ...)

Arguments

x	a MotifList object.
subset	a logical expression whose terms are predicates on the column names of the metadata table
select, drop, ...	these are ignored, appearing here only in fidelity to the generic definition of the method.

Value

A list of the matrices whose metadata satisfies the supplied subset

Author(s)

Paul Shannon

See Also

MotifDb, query, export, flyFactorSurvey, hPDI, jaspar, ScerTF, uniprobe

Examples

  mdb <- MotifDb
  if (interactive ()) {
    matrices <- subset (mdb, dataSource=='UniPROBE')
    egr1.matrices <- subset (mdb, geneSymbol=='Egr1')
    jaspar.egr1.matrices <- subset (mdb, geneSymbol=='Egr1' &
                                         dataSource == 'JASPAR_CORE')
      # one of the mouse egr1 matrices has a geneSymbol 'Zif268', but
      # has the proper entrez geneId.  
    all.egr1.matrices <- subset (mdb, geneId=='13653')
    }

PriceLab/MotifDb documentation built on March 23, 2022, 7:42 p.m.