| 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)
}