SchemeTreeSet-class {xps}R Documentation

Class SchemeTreeSet

Description

This class provides the link to the ROOT scheme file and the ROOT trees contained therein. It extends class TreeSet.

Objects from the Class

Objects can be created using the functions import.expr.scheme, import.exon.scheme, import.genome.scheme or root.scheme.

Slots

chipname:
Object of class "character" representing the Affymetrix chip name.
chiptype:
Object of class "character" representing the chip tpye, either ‘GeneChip’, ‘GenomeChip’ or ‘ExonChip’.
probeinfo:
Object of class "list" representing chip information, including nrows, ncols, number of probes, etc.
mask:
Object of class "data.frame". The data.frame can contain the mask used to identify the probes as e.g. PM, MM or control probes.
setname:
Object of class "character" representing the name to the ROOT file subdirectoy where the ROOT scheme trees are stored; it is identical to chipname.
settype:
Object of class "character" describing the type of treeset stored in setname, i.e. ‘scheme’.
rootfile:
Object of class "character" representing the name of the ROOT scheme file, including full path.
filedir:
Object of class "character" describing the full path to the system directory where rootfile is stored.
numtrees:
Object of class "numeric" representing the number of ROOT trees stored in subdirectoy setname.
treenames:
Object of class "list" representing the names of the ROOT trees stored in subdirectoy setname.

Extends

Class "TreeSet", directly.

Methods

attachMask
signature(object = "SchemeTreeSet"): exports scheme tree from ROOT scheme file and and saves as data.frame mask.
chipMask
signature(object = "SchemeTreeSet"): extracts data.frame mask.
chipMask<-
signature(object = "SchemeTreeSet", value = "data.frame"): replaces data.frame mask.
chipName
signature(object = "SchemeTreeSet"): extracts slot chipname.
chipType
signature(object = "SchemeTreeSet"): extracts slot chiptype.
chipType<-
signature(object = "SchemeTreeSet", value = "character"): replaces slot chiptype.
export
signature(object = "SchemeTreeSet"): exports ROOT trees as text file, see export-methods.
ncols
signature(object = "SchemeTreeSet"): extracts the physical number of array columns from slot probeinfo.
nrows
signature(object = "SchemeTreeSet"): extracts the physical number of array rows from slot probeinfo.
probeInfo
signature(object = "SchemeTreeSet"): extracts slot probeinfo.
removeMask
signature(object = "SchemeTreeSet"): replaces data.frame mask with an empty data.frame of dim(0,0).

Author(s)

Christian Stratowa

Examples

showClass("SchemeTreeSet")

[Package xps version 1.2.10 Index]