# This package extends the capabilities of affylmGUI graphical interface. Affymetrix 3' IVT, gene an exon arrays are actually implemented togheter with Illumina, GEO matrix series files and tab delimited files.

## Documentation for package ‘oneChannelGUI’ version 1.8.10

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A B C D E F G H I L M N O P R S T U V W

## -- --

oneChannelGUI-package | Set of functions extending the capability of affylmGUI package

## -- --

.annotation | Starting oneChannelGUI package

## -- A --

AboutaffylmGUI | Starting oneChannelGUI package
AboutextendedaffylmGUI | Starting oneChannelGUI package
addAnnLib | Starting oneChannelGUI package
affyPLMHelp | Starting oneChannelGUI package
affyPlotMA | Starting oneChannelGUI package
aptFolder | Starting oneChannelGUI package
AptMidas | Graphical interface to APT midas

## -- B --

biomartFilter | Filtering only gene-level probe sets with multiple ensembl transcripts
buildingLocalAnnotation | Updates local gene-level annotation data for gene and exon arrays using the netaffx database

## -- C --

changeMenu | Starting oneChannelGUI package
changes | Starting oneChannelGUI package
chooseEDir | Starting oneChannelGUI package
colExtract | Extract a column from a tab delimited file with header
combineGeoMSF | This function allows to combine GEO Matrix Series Files belonging to the same experiment.
ComputeContrasts | Starting oneChannelGUI package
ComputeLinearModelFit | Starting oneChannelGUI package
consistentFilters | This function allows filtering using the combination of multiple paramenters, e.g. MiDAS p-values and Rank Product p-values
createGeoTarget | Creating a affylmGUI Target starting from a GEO Matrix series file
crosshybFilter | Removing from exon array gene/exon level probe sets characterized by cross hybridization with other transcripts
crosshybhuex.annotation | Cross hybriduzation data for exon CORE subset of human exon array 1.0 ST
crosshybmoex.annotation | Cross hybriduzation data for exon CORE subset of mouse exon array 1.0 ST
crosshybraex.annotation | Cross hybriduzation data for exon CORE subset of rat exon array 1.0 ST

## -- D --

dabgFilter | Starting oneChannelGUI package
delete.ML | Starting oneChannelGUI package
deleteLocalData | Starting oneChannelGUI package
dfMAplot | MA and Volcano plots from data present in a limma derived topTable

## -- E --

EG2probeset | This function allows to link GeneBank and Entrez Gene ids to gene-level probe set ids
erankProdAltSpl | Implementation of the Rank Product method for the detection of alternative splicing events
erankProdAltSplFilter | Filtering Rank Product results for the detection of alternative splicing events
exonsSpecific2as | Defining the exons associated to the various alternative isoforms
ExportfeatureNames | Starting oneChannelGUI package
ExportNormalizedExpressionValues | Starting oneChannelGUI package
ExportNormalizedExpressionValues1 | Starting oneChannelGUI package
extractAffyids | Extracting probe ids associated to a specific Gene Ontology term

## -- F --

filteringTable | Filtering a tab delimited file

## -- G --

geneExonLibs | Download the Library files for gene and exon analysis
genefilterHelp | Starting oneChannelGUI package
geoVSbioc | linking GEO platforms to available BioC annotations libraries
GetNormalizationMethod | Starting oneChannelGUI package
GOenrichment | Searching for Gene Ontology enriched terms within a set of differentially expressed genes
GOstatsHelp | Starting oneChannelGUI package

## -- H --

huex.annotation | Annotation data for CORE subset of human exon array 1.0 ST
hugene.annotation | Annotation data for human gene array 1.0 ST

## -- I --

initialize.extAffylmGUI | Starting oneChannelGUI package
inspecting.one.splice.index | Plotting on the profiles of splice indexes for a transcript cluster ID
inspecting.splice.index | Plotting on a pdf file the profiles of splice indexes
intensityFilter | intensity filtering with a mouse click
intronicBg | Starting oneChannelGUI package
IPAlistFilter | Filtering an expression set using a set of Entrez genes extracted from Ingenuity Pathways analysis (IPA)
iqrFilter | Interquantile filtering with a mouse click

## -- L --

largedatasetNorm | Starting oneChannelGUI package
libraryFilesDir | Starting oneChannelGUI package
listFilter | Subsetting an expression set using a list of Affymetrix ids

## -- M --

mapping2ensembl | Associating e-level probe sets to entrez gene exonic structure
mapping2exon | This function maps on exon-level Probe Selection Region (PSR) starting for the file produced by function oneChannelGUI: Mapping exon level probe sets to Reference Sequences
mapping2RefSeq | This function maps on NCBI Reference sequences spliced exons detected by the function oneChannelGUI: Inspecting splice indexes
masigpro | The function executes maSigPro analysis
masigpro.edesign | The function creates an edesign object needed to run maSigPro
masigpro.view | The function allows the visualization of maSigPro results
maSigProHelp | Starting oneChannelGUI package
metaArrayIC | Graphical interface to metaArray Integrative Correlation function
metaArrayMerge | Tool to create a merge object for metaArray package
midasFilter | Starting oneChannelGUI package
ML.edesign | The function creates an data frame containing the parameters useful for class prediction
moex.annotation | Annotation data for CORE subset of mouse exon array 1.0 ST
mogene.annotation | Annotation data for mouse gene array 1.0 ST
myExpresso | Running the affy expresso function with the widget

## -- N --

NewLimmaFile | Starting oneChannelGUI package
NormalizeNow | Starting oneChannelGUI package
normBoxplot | Box plot of the arrays data available in NormalizeAffyData slot

## -- O --

ocPlotHist | Gene/Exon level density plots
ocPlotPCA | Gene/Exon level density plots
oneChannelGUI | Set of functions extending the capability of affylmGUI package
oneChannelGUI.start | Starting oneChannelGUI package
oneChannelGUIHelp | Starting oneChannelGUI package
OpenAFile | Starting oneChannelGUI package
OpenAGeoFile | Starting oneChannelGUI package
OpenALimmaFile | Starting oneChannelGUI package
OpenBeadStudioFiles | Read BeadStudio expression data file
OpenCDFandTargetsfiles | Starting oneChannelGUI package
OpenExonandTargetsfiles | Starting oneChannelGUI package
OpenExonFile | Starting oneChannelGUI package
OpenExonProbeFile | Starting oneChannelGUI package
OpenGeoFile | Starting oneChannelGUI package
OpenGeoFiles | Starting oneChannelGUI package
OpenLargeFile | Starting oneChannelGUI package
OpenLargefiles | This function loads large data set made from tab delimited files
OpenLimmaFile | Starting oneChannelGUI package

## -- P --

pamrHelp | Starting oneChannelGUI package
pdmclassHelp | Starting oneChannelGUI package
plierToZero | Setting to 0 low log2 intensity values generated with plier
plotGO | Plotting parents of a GO term with few mouse click
PlotOptionsv1 | A modified version of the function used in affyPLM library

## -- R --

raex.annotation | Annotation data for CORE subset of rat exon array 1.0 ST
ragene.annotation | Annotation data for rat gene array 1.0 ST
rankProd | graphical interface to rank product method implemented in RankProd Bioconductor library.
RankProdHelp | Starting oneChannelGUI package
rawBoxplotPN | Plotting raw log2 intensities from controls
rawpCheck | Raw p-value distribution from limma analysis by a mouse click
recoverUnfiltered | Starting oneChannelGUI package
refseqDownload | Retrieving Reference Sequences from NCBI ftp
retrievePSRseq | This function, given a file containing exon-level probesets retrieves Probe selection Regions, PRS, from RRE db
reviqrFilter | Reverse interquantile filtering with a mouse click

## -- S --

sample.size.evaluation | The function executes and plots results from ssize and delta fulction from the ssize packahe
sample.size.evaluation1 | The function executes functions from the sizepower packahe
SaveAsLimmaFile | Starting oneChannelGUI package
SetED | Starting oneChannelGUI package
showDataset | Grabbing info about the available expression set
showTopTable | Modification of the function immplemented in affylmGUI to generate a topTable
siggenes | The function executes SAM analysis implemented in siggenes bioconductor library
siggenesHelp | Starting oneChannelGUI package
simFilter | This function allows filtering on the basis of the average splice index mean or min difference between two groups
sizepowerHelp | Starting oneChannelGUI package
spliceIndex | This function coverts the exon intenisty data in a slice index
ssizeHelp | Starting oneChannelGUI package

## -- T --

targetWidget | Widget to create a target file to load .CEL files
templA | Generating a template A to be uploaded in Ingenuity Pathways analysis (IPA)
trainTest | Creating a training set and a test set by a mouse click

## -- U --

updateLibs | This function allows to update the present installation of Bioconductor

## -- V --

VennDiagram | Venn diagrams using two or three lists

## -- W --

whichKindOfArray | Starting oneChannelGUI package