mappings {exonmap}R Documentation

Map between probes, probesets, exons, transcripts and genes

Description

A set of functions of the form X.to.Y. That take a character vector of database identifiers of type X, and return a set of type Y, either as a character vector, or as rows in a dataframe.

Usage


probeset.to.probe(v,as.vector=TRUE,unique=TRUE,mt.rm=TRUE)
probeset.to.exon(v,as.vector=TRUE,unique=TRUE,subset=c("core","est","prediction"))
probeset.to.transcript(v,as.vector=TRUE,unique=TRUE,subset=c("core","est","prediction"))
probeset.to.gene(v,as.vector=TRUE,unique=TRUE,subset=c("core","est"))
exon.to.probeset(v,as.vector=TRUE,unique=TRUE,subset=c("core","est","prediction"),probes.min=4)
exon.to.transcript(v,as.vector=TRUE,unique=TRUE,subset=c("core","est","prediction"))
exon.to.gene(v,as.vector=TRUE,unique=TRUE,subset=c("core","est"))
transcript.to.probeset(v,as.vector=TRUE,unique=TRUE,subset=c("core","est","prediction"),probes.min=4)
transcript.to.exon(v,as.vector=TRUE,unique=TRUE,subset=c("core","est","prediction"))
transcript.to.gene(v,as.vector=TRUE,unique=TRUE,subset=c("core","est"))
gene.to.probeset(v,as.vector=TRUE,unique=TRUE,subset=c("core","est"),probes.min=4)
gene.to.exon(v,as.vector=TRUE,unique=TRUE,subset=c("core","est"))
gene.to.transcript(v,as.vector=TRUE,unique=TRUE,subset=c("core","est"))
symbol.to.gene(v,as.vector=TRUE,unique=TRUE)
gene.to.exon.probeset(v,unique=TRUE,probes.min=4)
gene.to.exon.probeset.expr(x,v,probes.min=4)
exon.to.sequence(v,as.vector=TRUE,unique=TRUE,subset=c("core","est"))

Arguments

v A character vector of database identifiers
as.vector If TRUE, return a character vector otherwise return a data.frame
unique If TRUE, remove duplicates from the results
mt.rm If TRUE, remove multitarget probesets before returning the result
probes.min Only return probesets with at least this many probes
subset Which subset of the database to perform the mapping against? core refers to Ensembl genes, est refers to Ensembl ESTs and prediction refers to Ensembl predictions.
x An ExpressionSet object or a matrix containing expression data. If the latter, then the rownames must specify the exon array probeset names.

Details

Connects to the X:Map database to retrieve data. Before these functions can be used, xmapConnect must have been called.

By default the results are returned as a vector, and duplicate entries are removed. Note that the function probeset.to.probe, by default, also removes multitarget probesets.

gene.to.exon.probeset generates a single data.frame with mappings between genes, exons and probesets. gene.to.exon.probeset.exprs does the same but adds the expression data for the corresponding probesets onto the beginning of the data.frame.

Mappings against the prediction subset of the database are made slightly more complicated since there are no predicted genes, only transcripts and exons. In addition, their IDs are integers not strings. The additional functions genscan.label.to.id and genescan.id.to.label should be used to provide the mapping between names of the form 'GENSCAN0000...' and the integer ids used for the transcripts.

Value

A character vector, or, if as.vector=FALSE, a data.frame.

Author(s)

C.J. Miller, M.J. Okoniewski

References

http://xmap.picr.man.ac.uk

See Also

xmapConnect filters details

Examples

  if(interactive()) {
    xmapConnect()
    probeset.to.gene(c("3743919"))
    probeset.to.gene(c("3743919"),as.vector=FALSE)
    probeset.to.gene(c("3743919","3743919"),as.vector=FALSE,unique=TRUE)
    gene <-  probeset.to.gene(c("3743919"))
    gene.to.probeset(gene,as.vector=TRUE)
    gene.to.exon.probeset(gene)
  }

[Package exonmap version 2.0.03 Index]