query: query

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

query

Description

A very general search tool, returning all matrices whose metadata, in ANY column, is matched by the query string.

Usage

## S4 method for signature 'MotifList'
query(object, andStrings, orStrings, notStrings, ignore.case=TRUE)

Arguments

object	a MotifList object.
andStrings	a character string vector, length one or more, every element of which must be found in the metadata
orStrings	a character string vector, length one or more, any element of which must be found in the metadata
notStrings	a character string vector, length one or more, none of which may appear in the metadata
ignore.case	a logical value, default TRUE

Value

A list of the matrices

Author(s)

Paul Shannon

See Also

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

Examples

  matrices.human <- query(MotifDb, 'hsapiens')
  matrices.sox4 <- query(MotifDb, 'sox4')
  uniprobe.sox.matrices <- query(MotifDb, c('uniprobe', 'sox'))
    # two approaches to selectinve extraction of TFEB matrices
  tfeb.human.1 <- query(MotifDb, andStrings=c("TFEB", "hsapiens"), notStrings=c("hpdi", "jolma", "cisbp"))
  tfeb.human.2 <- query(MotifDb, andStrings=c("TFEB", "hsapiens"), orStrings=c("hocomoco", "jaspar", "swissregulon"),
                        notStrings="2016")

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