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xps (version 1.26.1)

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

Description

The package handles pre-processing, normalization, filtering and analysis of Affymetrix GeneChip expression arrays, including exon arrays (Exon 1.0 ST: core, extended, full probesets), gene arrays (Gene 1.0 ST) and plate arrays on computers with 1 GB RAM only. It imports Affymetrix .CDF, .CLF, .PGF and .CEL as well as annotation files, and computes e.g. RMA, MAS5, FARMS, DFW, FIRMA, tRMA, MAS5-calls, DABG-calls, I/NI-calls. It is an R wrapper to XPS (eXpression Profiling System), which is based on ROOT, an object-oriented framework developed at CERN. Thus, the prior installation of ROOT is a prerequisite for the usage of this package, however, no knowledge of ROOT is required. ROOT is licensed under LGPL and can be downloaded from http://root.cern.ch.

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Version

Version

1.26.1

License

GPL (>= 2.0)

Maintainer

Christian Stratowa

Last Published

February 15th, 2017

Functions in xps (1.26.1)

AnalysisTreeSet-class

Class AnalysisTreeSet

attachBgrd-methods

Attach/Remove Background Intensities

attachDataXY-methods

Attach/Remove (X,Y)-Coordinates

attachExpr-methods

Attach/Remove Expression Measures

Functions to assess RNA Degradation.

addData-methods

Import additional CEL files into a DataTreeSet

attachInten-methods

Attach/Remove Intensities

attachMask-methods

Attach/Remove Scheme Mask

attachData-methods

Attach/Remove Data

attachCall-methods

Attach/Remove Detecion Call Measures

coiplot-methods

Center-Of-Intensity QC Plots

corplot-methods

Array-Array Expression Level Correlation Plot

attachUnitNames-methods

Attach/Remove Unit Names

callplot-methods

Barplot of Percent Present and Absent Calls.

attachProbe-methods

Attach/Remove Probe Sequence and/or GC Content

CallTreeSet-class

Class CallTreeSet

Background Correction

borderplot-methods

Plots of Border Elements

callFilter-methods

Detection Call Filter

boxplot-methods

cvFilter-methods

Coefficient of Variation Filter

Factor Analysis for Robust Microarray Summarization Expression Measure

Detection Above Background Call

fcFilter-methods

Fold-Change Filter

Distribution Free Weighted Expression Measure

DataTreeSet-class

Class DataTreeSet

ExprTreeSet-class

Class ExprTreeSet

Get Extension of Tree Names

Get Splice Score from FIRMA

Functions for fitting probe-level models

Informative/Non-Informative Call

initialize-methods

Initialize Classes

mboxplot-methods

Box Plots of Relative M Values

MAS 5.0 Expression Measure

Get Number of Trees

Plot Image(s) for Device

Get Probe Information

Display an Image

Import CEL files into a DataTreeSet

Create MetaProbeset File for APT

mvaplot-methods

plotIntensity2GC

Boxlot of Probe Intensities Stratified by GC Content for Device.

Plot Density Estimate for Device

Test for Existing ROOT File

Compute expression levels from raw data

diffFilter-methods

Difference Filter

Get/Set Expression Values

import.exon.scheme

Import CLF, PGF and annotation files into a SchemeTreeSet

madFilter-methods

Median Absolute Deviation Filter

import.expr.scheme

Import CDF, probe and annotation files into a SchemeTreeSet

madplot-methods

Array-Array Expression Level Distance Plot

probesetplot-methods

Plot of Probe Intensities for a Probeset.

Box Plots of Relative Log Expression (RLE) for Device

Plot of Probe Intensities for a Probeset for Device.

highFilter-methods

Upper Threshold Filter

Plot Density Estimate

intensity2GCplot-methods

Boxlot of Probe Intensities Stratified by GC Content.

intensity-methods

Get/Set Data Values

Plots of Border Elements for Device

pcaplot-methods

Array-Array Expression Level Distance Plot for Device

presCall-methods

Get/Set Present Call Values

PreFilter-class

Class PreFilter

Barplot of PM and MM Intensities.

probeContentGC-methods

Get G/C Content for Probes

rawCELName-methods

Method for getting names of the raw CEL-files

Conversion of Parameter exonlevel to Integer

Relative Log Expression (RLE)

Export filter data as text files

Get Expression Levels from FIRMA

gapFilter-methods

Finding Isoforms using Robust Multichip Analysis

Functions for fitting RMA as probe-level model

getTreeData-methods

Export Tree Data

ROOT Profile Plot

Create class SchemeTreeSet accessing ROOT scheme file

validCall-methods

Get Valid Detection Call Values

validData-methods

Extract Subset of Data

Box Plots of Normalized Unscaled Standard Errors (NUSE) for Device

ProjectInfo-constructor

Constructor for Class ProjectInfo

Create class ExprTreeSet accessing ROOT expression file

Create class CallTreeSet accessing ROOT detection call file

root.browser-methods

Open the ROOT object browser

ProjectInfo-class

Class ProjectInfo

transposed Robust Multi-Array Average Expression Measure

Export data as text files

Export data from ROOT file

Base Class Filter

Get Chip Name and Type

FilterTreeSet-class

Class FilterTreeSet

import.genome.scheme

Import CLF, PGF and annotation files into a SchemeTreeSet

MvA Scatter Plot for Device

PreFilter-constructor

Constructor for Class PreFilter

Function for Applying a PreFilter to an ExprTreeSet

Probe Set Quality Control Functions

QualTreeSet-class

Class QualTreeSet

ROOT 1D-Histogram

validExpr-methods

Get Valid Expression Levels

ProcesSet-class

Class ProcesSet

validSE-methods

Get Valid Standard Errors

Create class DataTreeSet accessing ROOT data file

ROOT Density Plot

ROOT 2D-Histogram

ROOT 3D-Histogram

indexUnits-methods

Convert Method Type to Tree Extension

MAS 5.0 Absolute Detection Call

MAS 4.0 Expression Measure

Normalization on Affymetrix Probe Level Data or on Expression Levels

Get Tree Names w/o Extension

Box Plots for Device

Barplot of Percent Present and Absent Calls for Device

UniFilter-class

Class UniFilter

Validate Tree Type

varFilter-methods

Variance Filter

PCA Plot for Device

Barplot of PM and MM Intensities for Device

Create Quality Assessment Report.

probeSequence-methods

Get Probe Sequence

probesetID2unitID-methods

Conversion between Probeset IDs and UnitIDs

rleplot-methods

Box Plots of Relative Log Expression (RLE)

Robust Multi-Array Average Expression Measure

root.merge.data

Create class DataTreeSet by merging ROOT data files

ROOT M vs A Plot

UniFilter-constructor

Constructor for Class UniFilter

Probe Set Summarizing Functions

SchemeTreeSet-class

Class SchemeTreeSet

Function for Applying an UniFilter to an ExprTreeSet

volcanoplot-methods

xps Package Overview

Test for ROOT File

lowFilter-methods

Lower Threshold Filter

Normalized Unscaled Standard Errors (NUSE)

Center-Of-Intensity QC Plots for Device

Array-Array Expression Level Correlation Plot for Device

nuseplot-methods

Box Plots of Normalized Unscaled Standard Errors (NUSE)

Methods for accessing perfect matches and mismatches

ratioFilter-methods

quantileFilter-methods

Quantile Filter

ROOT An Object-Oriented Data Analysis Framework

treeInfo-methods

Get UserInfo from ROOT Trees

symbol2unitID-methods

Conversion between Gene Symbols and UnitIDs

uniTest-methods

A Two-Group Unitest

unitestFilter-methods