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

Arguments

X Vector of identifiers to map (e.g. an ensembl gene id)
db Return data from the Ensembl gene database (default), from genscan predictions or from the EST subset of Ensembl?
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
symbol.db The name of the database containing the gene symbol to map to probeset or gene (e.g. hugo, UniProt, etc.)

Details

Connects to the X:MAP database to retrieve data. For Ensembl genes and genscan predictions, xmapDatabase() must be called first. ESTs are stored in a separate 'extras' database. To use the EST data xmapExtras() must be called in addition to xmapDatabase(), to set up the connection.

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/

See Also

xmapDatabase xmapExtras

Examples

 
  ## Not run: 
library(exonmap)
#reading arrays etc.
#x  <- read.exon()

data(exonmap)
xmapDatabase("Human")

cmp <- pc(x.rma,"group",c("a","b"))

fc.r <-fc(cmp)
tt.r <-tt(cmp)

# Only a test! - and x doesn't have many genes in it!
keep.fc <- abs(fc.r) > 1
keep.tt <- tt.r < 0.05

keep <- keep.fc & keep.tt

ps <- featureNames(x.rma)[keep]

# OK, test mapping functions

ex <- probeset.to.exon(ps)
tr <- probeset.to.transcript(ps)
ge <- probeset.to.gene(ps)

probeset.to.exon(ps,list.out=TRUE)
probeset.to.transcript(ps,list.out=TRUE)
probeset.to.gene(ps,list.out=TRUE)

exon.to.transcript(ex)
exon.to.gene(ex)
exon.to.probeset(ex)

transcript.to.gene(tr)
transcript.to.exon(tr)
transcript.to.probeset(tr)

gene.to.transcript(ge)
gene.to.exon(ge)
gene.to.probeset(ge)

gds <- gene.details(ge)
trs <- transcript.details(tr)
exs <- exon.details(ex)
pss <- probeset.stats(ps)

symbol.to.gene(unlist(gds[,13]))
symbol.to.probeset(unlist(gds[,13]))

genes.in.range(1,100000,1,1)
genes.in.range(1,100000,-1,1)

transcripts.in.range(1,100000,1,1)
transcripts.in.range(1,100000,-1,1)

exons.in.range(1,100000,1,1)
exons.in.range(1,100000,-1,1)

probesets.in.range(1,100000,1,1)
probesets.in.range(1,100000,-1,1)

probeset.stats(ps)
## End(Not run)

[Package exonmap version 1.4.3 Index]