SchemeTreeSet-class: Class SchemeTreeSet

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

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.

unitname:

Object of class "data.frame". The data.frame can contain the mapping between the internal UNIT_IDs and the UnitNames, i.e. the probeset IDs.

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.

probe:

Object of class "data.frame". The data.frame can contain the probe info for the oligos as e.g. probe sequence, G/C content.

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.

attachProbe

signature(object = "SchemeTreeSet"): exports probe tree from ROOT scheme file and and saves varlist as data.frame probe.

attachProbeContentGC

signature(object = "SchemeTreeSet"): exports probe tree from ROOT scheme file and and saves fNumberGC as data.frame probe.

attachProbeSequence

signature(object = "SchemeTreeSet"): exports probe tree from ROOT scheme file and and saves fSequence as data.frame probe.

attachUnitNames

signature(object = "SchemeTreeSet"): exports unit tree from ROOT scheme file and and saves as data.frame unitname.

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.

chipProbe

signature(object = "SchemeTreeSet"): extracts data.frame probe.

chipProbe<-

signature(object = "SchemeTreeSet", value = "data.frame"): replaces data.frame probe.

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.

probeContentGC

signature(object = "SchemeTreeSet"): extracts all or selected GC contents from data.frame probe.

probeInfo

signature(object = "SchemeTreeSet"): extracts slot probeinfo.

probeSequence

signature(object = "SchemeTreeSet"): extracts all or selected probe sequences from data.frame probe.

probesetID2unitID

signature(object = "SchemeTreeSet"): extracts all or selected probesetIDs from data.frame unitname with UnitName, i.e. probeset ID, as (row)names.

removeMask

signature(object = "SchemeTreeSet"): replaces data.frame mask with an empty data.frame of dim(0,0).

removeProbe

signature(object = "SchemeTreeSet"): replaces data.frame probe with an empty data.frame of dim(0,0).

removeProbeContentGC

signature(object = "SchemeTreeSet"): replaces data.frame probe with an empty data.frame of dim(0,0).

removeProbeSequence

signature(object = "SchemeTreeSet"): replaces data.frame probe with an empty data.frame of dim(0,0).

removeUnitNames

signature(object = "SchemeTreeSet"): replaces data.frame unitname with an empty data.frame of dim(0,0).

symbol2unitID

signature(object = "SchemeTreeSet"): extracts internal UNIT_ID(s) for one or more gene symbols.

transcriptID2unitID

signature(object = "SchemeTreeSet"): extracts all or selected transcriptIDs from data.frame unitname with UnitName, i.e. transcript ID, as (row)names.

unitID2probesetID

signature(object = "SchemeTreeSet"): extracts all or selected unitIDs from data.frame unitname with UNIT_ID as (row)names.

symbol2unitID

signature(object = "SchemeTreeSet"): extracts gene symbols for one or more internal UNIT_ID(s).

unitID2transcriptID

signature(object = "SchemeTreeSet"): extracts all or selected unitIDs from data.frame unitname with UNIT_ID as (row)names.

unitNames

signature(object = "SchemeTreeSet"): extracts data.frame unitname.

unitNames<-

signature(object = "SchemeTreeSet", value = "data.frame"): replaces data.frame unitname.

Author(s)

Christian Stratowa

Examples

showClass("SchemeTreeSet")

xps documentation built on Nov. 8, 2020, 6 p.m.