mappings {exonmap} | R Documentation |
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.
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"))
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. |
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.
A character vector, or, if as.vector=FALSE
, a data.frame
.
C.J. Miller, M.J. Okoniewski
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) }