| 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")