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) 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)
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.) |
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.
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: 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)