probeset.to.probe {exonmap}R Documentation

Use the X:MAP database to translate between genes, transcripts, exons, probesets and probes

Description

Each of the functions is in the form X.to.Y, and takes a list of identifiers for the things of type X and returns the corresponding things of type Y.

Usage

  probeset.to.probe(X,list.out=FALSE, drop.mt=FALSE,  debug=0)
  probeset.to.exon(X,list.out=FALSE, vector.out=TRUE, unique=TRUE, drop.mt=FALSE, debug=0) 
  probeset.to.transcript(X, list.out=FALSE, vector.out=TRUE, unique=TRUE, drop.mt=FALSE, debug=0) 
  probeset.to.gene(X,list.out=FALSE, vector.out=TRUE,symbols.out=FALSE, unique=TRUE, drop.mt=FALSE, debug=0) 
  exon.to.probeset(X, list.out=FALSE, vector.out=TRUE, unique=TRUE, probes.min=4, debug=0) 
  exon.to.transcript(X,list.out=FALSE, vector.out=TRUE, unique=TRUE, debug=0) 
  exon.to.gene(X,list.out=FALSE, vector.out=TRUE, unique=TRUE, debug=0) 
  transcript.to.exon(X, list.out=FALSE,vector.out=TRUE, unique=TRUE, debug=0) 
  transcript.to.probeset(X, list.out=FALSE,vector.out=TRUE, unique=TRUE, probes.min=4,  debug=0)
  transcript.to.gene (X, list.out=FALSE, vector.out=TRUE, unique=TRUE, debug=0) 
  gene.to.exon(X, list.out=FALSE, vector.out=TRUE, unique=TRUE, debug=0)   
  gene.to.probeset(X, list.out=FALSE, vector.out=TRUE, unique=TRUE, probes.min=4,  debug=0) 
  symbol.to.probeset(X, vector.out=TRUE,db=c("hugo","symbol","UniProt","RefSeqPeptide","RFAM","UniProtSpliceVariant","miRNA"),probes.min=4, debug=0)
  symbol.to.gene(X, debug=0) 

Arguments

X Vector of identifiers to map (e.g. an ensembl gene id)
list.out If TRUE, results are presented as a list. Overrides effects of vector.out and symbols.out
vector.out By default, return only the names of the mapped identifiers, if FALSE, return a summary table
symbols.out If TRUE, returns just gene symbols
unique If TRUE, pre-filters the data to remove dublicates
drop.mt Filter out multi-targeting probesets prior to database search
probes.min Only return probesets that hit the genome with at least this number of probes
db The name of the symbol database to search when looking for the Ensembl gene identifier
debug nything other than 0 returns debugging information. Verbosity increases with value

Details

Value

Vector of probeset names, or a data frame with probeset names and number of probe hits.

Author(s)

Michal Okoniewski

References

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

Examples

 
  ## Not run: 
    genes <- probeset.to.gene("2326601"); 
    genes <- probeset.to.gene(c("2326780","2326822" )); 
    genes <- probeset.to.gene(c("2326780","2326822"), vector.out=FALSE, probes.min=1); # produces a table of results, with genes matched by the probesets. 
  
## End(Not run)

[Package exonmap version 1.0.07 Index]