SchemeTreeSet-class {xps} | R Documentation |
This class provides the link to the ROOT
scheme file and
the ROOT
trees contained therein. It extends class TreeSet
.
Objects can be created using the functions import.expr.scheme
,
import.exon.scheme
, import.genome.scheme
or root.scheme
.
chipname
:"character"
representing the Affymetrix
chip name.chiptype
:"character"
representing the chip tpye,
either ‘GeneChip’, ‘GenomeChip’ or ‘ExonChip’.probeinfo
:"list"
representing chip information,
including nrows, ncols, number of probes, etc.mask
:"data.frame"
. The data.frame can contain the mask
used to identify the probes as e.g. PM, MM or control probes.setname
:"character"
representing the name to the
ROOT
file subdirectoy where the ROOT
scheme trees are stored;
it is identical to chipname
.settype
:"character"
describing the type of treeset
stored in setname
, i.e. ‘scheme’.rootfile
:"character"
representing the name
of the ROOT
scheme file, including full path.filedir
:"character"
describing the full path to
the system directory where rootfile
is stored.numtrees
:"numeric"
representing the number of
ROOT
trees stored in subdirectoy setname
.treenames
:"list"
representing the names of the
ROOT
trees stored in subdirectoy setname
.
Class "TreeSet"
, directly.
signature(object = "SchemeTreeSet")
: exports scheme tree from
ROOT
scheme file and and saves as data.frame mask
.signature(object = "SchemeTreeSet")
: extracts data.frame mask
.signature(object = "SchemeTreeSet", value = "data.frame")
: replaces
data.frame mask
.signature(object = "SchemeTreeSet")
: extracts slot chipname
.signature(object = "SchemeTreeSet")
: extracts slot chiptype
.signature(object = "SchemeTreeSet", value = "character")
: replaces
slot chiptype
.signature(object = "SchemeTreeSet")
: exports ROOT
trees
as text file, see export-methods
.signature(object = "SchemeTreeSet")
: extracts the physical number of
array columns from slot probeinfo
.signature(object = "SchemeTreeSet")
: extracts the physical number of
array rows from slot probeinfo
.signature(object = "SchemeTreeSet")
: extracts slot probeinfo
.signature(object = "SchemeTreeSet")
: replaces data.frame mask
with an empty data.frame of dim(0,0).Christian Stratowa
showClass("SchemeTreeSet")