Description Arguments Details Value Note Author(s) See Also Examples
Attach/remove detection call and detection p-value to/from CallTreeSet
.
Usage
attachCall(object, treenames = "*")
attachPVal(object, treenames = "*")
removeCall(object)
removePVal(object)
object |
Object of class |
treenames |
Object of class |
By default detection calls will be saved in class CallTreeSet
in slots
data
and detcall
, respectively, since usually the data.frame
s obtained as
result of e.g. mas5.call
are of reasonable size. However, when computing many
arrays, especially exon arrays at probeset levels, it may be better to compute detection
calls with slot add.data=FALSE
thus avoiding memory problems. In this case, functions
attachCall
and attachPVal
allow to fill slots detcall
and data
,
respectively, on demand.
attachCall
exports detection calls from call trees from ROOT
call
file and and saves as data.frame detcall
. treenames
is a vector of
tree names to attach; for treenames="*"
all trees from slot treenames
will be exported and detection calls attached as data.frame detcall
.
attachPVal
exports detection p-values from call trees from ROOT
call
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 detection p-values attached as data.frame data
.
removeCall
removes detection calls from CallTreeSet
and replaces
data.frame detcall
with an empty data.frame of dim(0,0).
removePVal
removes detection p-values from CallTreeSet
and replaces
data.frame data
with an empty data.frame of dim(0,0).
A CallTreeSet
object.
Do not use attachCall
and attachPVal
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ## 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="/"))
## MAS5 detection call
call.mas5 <- mas5.call(data.test3,"tmp_Test3Call0",tmpdir="",add.data=FALSE,verbose=FALSE)
## attach data
call.mas5 <- attachPVal(call.mas5)
call.mas5 <- attachCall(call.mas5)
## get data.frames
pval.mas5 <- pvalData(call.mas5)
pres.mas5 <- presCall(call.mas5)
head(pval.mas5)
head(pres.mas5)
## remove data
call.mas5 <- removePVal(call.mas5)
call.mas5 <- removeCall(call.mas5)
rm(scheme.test3, data.test3)
gc()
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.