probeset.to.probe {exonmap} | R Documentation |
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.
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)
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 |
Vector of probeset names, or a data frame with probeset names and number of probe hits.
Michal Okoniewski
http://bioinformatics.picr.man.ac.uk/
## 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)