filters {exonmap} | R Documentation |
Given a character vector of probeset names, filter it to keep (or
exclude) those probesets that are mapped by X:Map to exons, introns,
intergenic regions or are annotated as containing potentially
cross-hybridizing (multitarget) probes. Functions of the form
is. ...
return a logical vector.
exonic(v,exclude=FALSE,mt.rm=TRUE) intronic(v,exclude=FALSE,mt.rm=TRUE) intergenic(v,exclude=FALSE,mt.rm=TRUE) multitarget(v,exclude=FALSE,mt.level=1) is.exonic(v) is.intronic(v) is.intergenic(v) is.multitarget(v,mt.level=1) select.probewise(v,filter=c("exonic","intronic","intergenic","multitarget"),mt.rm=TRUE,mt.level=1) exclude.probewise(v,filter=c("exonic","intronic","intergenic","multitarget"),mt.rm=TRUE,mt.level=1)
v |
A character vector of probeset names identifiers |
exclude |
If TRUE, remove (rather than keep) matching probesets, from the list. |
mt.rm |
If TRUE, remove multitarget probesets before returning the result |
mt.level |
The amount of multitargeting needed before a probeset is removed. See the package vignette for more details on how this number is calculated. |
filter |
What sort of probeset should be retained/removed? |
Connects to the X:Map database to retrieve data. Before these
functions can be used, xmapConnect
must have been
called.
By default, multitarget probesets are removed.
A character vector of filtered names.
C.J. Miller, M.J. Okoniewski
if(interactive()) { xmapConnect() gene <- probeset.to.gene(c("3743919")) ps <- gene.to.probeset(gene,as.vector=TRUE) exonic(ps) intronic(ps) intergenic(ps) multitarget(ps) exonic(ps,exclude=TRUE) intronic(ps,exclude=TRUE) intergenic(ps,exclude=TRUE) multitarget(ps,exclude=TRUE,mt.level=1) #or select.probewise(ps,"exonic") #etc.. exclude.probewise(ps,"exonic") #etc.. is.exonic(ps) is.intronic(ps) is.intergenic(ps) is.multitarget(ps) is.multitarget(ps,mt.level=4) }