DataTreeSet-class: Class DataTreeSet

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 data file and the ROOT trees contained therein. It extends class ProcesSet.

Objects from the Class

Objects can be created using the functions import.data or root.data.

Slots

bgtreenames:

Object of class "list" representing the names of optional ROOT background trees.

bgrd:

Object of class "data.frame". The data.frame can contain background intensities stored in ROOT background trees.

projectinfo:

Object of class "ProjectInfo" containing information about the project.

scheme:

Object of class "SchemeTreeSet" providing access to ROOT scheme file.

data:

Object of class "data.frame". The data.frame can contain the data (e.g. intensities) stored in ROOT data trees.

params:

Object of class "list" representing relevant parameters.

setname:

Object of class "character" representing the name to the ROOT file subdirectoy where the ROOT data trees are stored, usually ‘DataTreeSet’.

settype:

Object of class "character" describing the type of treeset stored in setname, usually ‘rawdata’.

rootfile:

Object of class "character" representing the name of the ROOT data 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 "ProcesSet", directly. Class "TreeSet", by class "ProcesSet", distance 2.

Methods

addData

signature(object = "DataTreeSet"): import additional CEL-files and update ROOT data file rootfile.

attachBgrd

signature(object = "DataTreeSet"): exports background trees from ROOT data file and and saves as data.frame bgrd.

attachDataXY

signature(object = "DataTreeSet"): exports (x,y)-coordinates from ROOT data file and and saves as data.frame data.

attachInten

signature(object = "DataTreeSet"): exports intensity trees from ROOT data file and and saves as data.frame data.

attachMask

signature(object = "DataTreeSet"): exports scheme tree from ROOT scheme file and and saves as data.frame mask of slot scheme.

attachProbeContentGC

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

attachUnitNames

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

background

signature(object = "DataTreeSet"): extracts slot bgrd.

background<-

signature(object = "DataTreeSet", value = "data.frame"): replaces slot bgrd.

bgtreeNames

signature(object = "DataTreeSet"): extracts slot bgtreenames.

indexUnits

signature(object = "DataTreeSet"): extracts (x,y)-coordinates and corresponding indices for all or selected unitIDs.

intensity

signature(object = "DataTreeSet"): extracts slot data.

intensity<-

signature(object = "DataTreeSet", value = "data.frame"): replaces slot data.

intensity2GCplot

signature(x = "DataTreeSet"): creates a boxplot of probe intensities stratified by GC content.

mm

signature(object = "DataTreeSet"): extracts the mismatch intensities.

mmindex

signature(object = "DataTreeSet"): extracts (x,y)-coordinates and corresponding MM indices for all or selected unitIDs.

ncols

signature(object = "DataTreeSet"): extracts the physical number of array columns from slot scheme.

nrows

signature(object = "DataTreeSet"): extracts the physical number of array rows from slot scheme.

pm

signature(object = "DataTreeSet"): extracts the perfect match intensities.

pmindex

signature(object = "DataTreeSet"): extracts (x,y)-coordinates and corresponding PM indices for all or selected unitIDs.

pmplot

signature(x = "DataTreeSet"): creates a barplot of mean perfect match and mismatch intensities.

probesetID2unitID

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

probesetplot

signature(x = "DataTreeSet"): creates a line plot of probe intensities for a probeset.

projectInfo

signature(object = "DataTreeSet"): extracts slot projectinfo.

projectInfo<-

signature(object = "DataTreeSet", value = "ProjectInfo"): replaces slot projectinfo.

rawCELName

signature(object = "DataTreeSet"): returns the name(s) of the imported raw CEL-files.

removeBgrd

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

removeDataXY

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

removeInten

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

removeMask

signature(object = "DataTreeSet"): replaces data.frame mask from slot scheme with an empty data.frame of dim(0,0).

removeProbeContentGC

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

removeUnitNames

signature(object = "DataTreeSet"): replaces data.frame unitname from slot scheme with an empty data.frame of dim(0,0).

symbol2unitID

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

transcriptID2unitID

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

unitID2probesetID

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

symbol2unitID

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

unitID2transcriptID

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

validBgrd

signature(object = "DataTreeSet"): extracts the valid data from data.frame bgrd.

validData

signature(object = "DataTreeSet"): extracts a subset of valid data from data.frame data.

xpsBgCorrect

signature(object = "DataTreeSet"): applies background correction methods. See bgcorrect.

xpsDABGCall

signature(object = "DataTreeSet"): computes DABG call.

xpsFIRMA

signature(object = "DataTreeSet"): computes FIRMA expression level and splice score.

xpsINICall

signature(object = "DataTreeSet"): computes I/NI call.

xpsMAS4

signature(object = "DataTreeSet"): computes MAS4 expression levels.

xpsMAS5

signature(object = "DataTreeSet"): computes MAS5 expression levels.

xpsMAS5Call

signature(object = "DataTreeSet"): computes MAS5 detection call.

xpsNormalize

signature(object = "DataTreeSet"): applies normalization methods.

xpsPreprocess

signature(object = "DataTreeSet"): applies normalization methods.

xpsQualify

signature(object = "DataTreeSet"): applies quality control methods.

xpsQualityControl

signature(object = "DataTreeSet"): applies quality control methods.

xpsRMA

signature(object = "DataTreeSet"): computes RMA expression levels.

xpsSummarize

signature(object = "DataTreeSet"): applies summarization methods.

Author(s)

Christian Stratowa

See Also

related classes ExprTreeSet, CallTreeSet.

Examples

showClass("DataTreeSet")

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