attachExpr-methods {xps} | R Documentation |
Attach/remove expression levels to/from ExprTreeSet
.
Usage
attachExpr(object, treenames = "*")
removeExpr(object)
object |
Object of class "ExprTreeSet" . |
treenames |
Object of class "list" representing the names of the
ROOT expression trees. |
By default expression levels will be saved in class ExprTreeSet
as slot
data
, since usually the data.frame
obtained as result of e.g. rma
normalization is of reasonable size. However, when normalizing many arrays, especially exon
arrays at probeset levels, it may be better to compute rma
with slot add.data=FALSE
thus avoiding memory problems. In this case, function attachExpr
allows to fill
slot data
on demand.
attachExpr
exports expression levels from expression trees from ROOT
expression file and and saves as data.frame data
. treenames
is a vector of
tree names to attach; for treenames="*"
all trees from slot treenames
will be exported and expression levels attached as data.frame data
.
removeExpr
removes expression levels from ExprTreeSet
and replaces
data.frame data
with an empty data.frame of dim(0,0).
A ExprTreeSet
object.
Do not use attachExpr
unless you know that your computer has sufficient RAM,
especially when using exon arrays. It may be advisible to use a subset of treenames
only.
Christian Stratowa
## first, load ROOT scheme file and ROOT data file scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/")) data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/")) data.rma <- rma(data.test3,"tmp_Test3RMA0",tmpdir="",background="pmonly",normalize=TRUE,add.data=FALSE,verbose=FALSE) ## attach data data.rma <- attachExpr(data.rma) ## get data.frame expr.rma <- validData(data.rma) head(expr.rma) ## remove data data.rma <- removeExpr(data.rma) rm(scheme.test3, data.test3) gc()