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. Next Generation Sequencing secondary analysis for ncRNA quantification is also available.


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Documentation for package ‘oneChannelGUI’ version 1.14.6

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

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

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.annotation Starting oneChannelGUI package
.myfindOverlaps Starting oneChannelGUI package
.myrk Starting oneChannelGUI package

-- A --

AboutaffylmGUI Starting oneChannelGUI package
AboutextendedaffylmGUI Starting oneChannelGUI package
addAnnLib Starting oneChannelGUI package
affyPLMHelp Starting oneChannelGUI package
affyPlotMA Starting oneChannelGUI package
annotateNGSeset Associate annotation to NGS data loaded in oneChannelGUI
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
chrLength Chromosomes lenghts
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
cosieHscore Parameters precalculated for the Affymetrix core human annotation subgroup from FMI Bioinformatics group and needed to correct SI
cosieHsfull Parameters precalculated for the Affymetrix full human annotation subgroup from FMI Bioinformatics group and needed to correct SI
cosieMmcore Parameters precalculated for the Affymetrix core mouse annotation subgroup from FMI Bioinformatics group and needed to correct SI
cosieMmfull Parameters precalculated for the Affymetrix full mouse annotation subgroup from FMI Bioinformatics group and needed to correct SI
cosieWrapper A wrapper to cosie, Corrected Splicing Indices for Exon arrays, that for any given set of new exon array experiments corrects for the observed bias and improves the detection of alternative splicing
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

-- 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

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edgerInterface graphical interface to edgeR library.
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
exonContrasts Defining t-test regularized p-values
exonsSpecific2as Defining the exons associated to the various alternative isoforms
exonTopTableExtract Extracts data on the basis of a defined t-test regularized p-value
exportFASTA Starting oneChannelGUI package
ExportfeatureNames Starting oneChannelGUI package
ExportNormalizedExpressionValues Starting oneChannelGUI package
ExportNormalizedExpressionValues1 Starting oneChannelGUI package
extractAffyids Extracting probe ids associated to a specific Gene Ontology term

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filteringTable Filtering a tab delimited file

-- G --

geneExonLibs Download the Library files for gene and exon analysis
genefilterHelp Starting oneChannelGUI package
genomePlot This function plots average intensity signals for two group experiment over the genes and transcripts structure mapped on ENSEMBL to identify a specific splicing event
geoVSbioc linking GEO platforms to available BioC annotations libraries
getNGSannotation Retrieving genome annotation from ENSEMBL
GetNormalizationMethod Starting oneChannelGUI package
GOenrichment Searching for Gene Ontology enriched terms within a set of differentially expressed genes
GOstatsHelp Starting oneChannelGUI package

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huex.annotation Annotation data for CORE subset of human exon array 1.0 ST
huex.variantexons table linking exon-level probe set ids to variant exons

-- 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
limma2paired graphical interface apply linear model to two sample groups with batch effect.
limmaExons graphical interface to limma for alternative splicing detection
listFilter Subsetting an expression set using a list of Affymetrix ids
log2Conversion Starting oneChannelGUI package

-- M --

makeBED15 This function creates files in BED15 format to be loaded on the UCSC browser
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
moex.variantexons table linking exon-level probe set ids to variant exons
myExpresso Running the affy expresso function with the widget

-- N --

ncHs.data Subset of genomic regions with ncRNA of Homo sapiens
ncMm.data Subset of genomic regions with ncRNA of Mus musculus
ncRn.data Subset of genomic regions with ncRNA in Rattus norvegicus
ncScaffold stand alone function to generate a scaffold containing only ncRNA location from ENSEMBL
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
OpenNgsfiles Starting oneChannelGUI package

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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
plotVariantSI This function plots on UCSC genome browser data derived by variantSI filter

-- R --

raex.annotation Annotation data for CORE subset of rat exon array 1.0 ST
raex.variantexons table linking exon-level probe set ids to variant exons
rankingConversion This function transforms intensity data in normalized ranks
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
refiningPeaks This function refines the structure of the genomics peaks, checking for the presence nearby peaks that cna be combined
reformatGdl This function reorganizes single NGS data in a matrix to be used for statistical analysis.
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
retrievePSRseq1gid This function, given a gene-level probeset id, retrieves Probe selection Regions, PRS, from RRE db
reviqrFilter Reverse interquantile filtering with a mouse click
runningJetta graphical interface to MADS/jetta R library.

-- 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
standAloneAddingAnnotation Attach to a data frame containing gene-level data derived from Affymetrix exon arrays the annotations derived by netaffx
standAloneBuildingLocalAnnotation Creates a data frame with gene-level annotation data for exon arrays using the netaffx database

-- 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 --

variantExons This function is used to generate a table containing exon-level probe set data linked to variant exons
variantSI This function allows filtering on the basis of variant exons
VennDiagram Venn diagrams using two or three lists

-- W --

whichKindOfArray Starting oneChannelGUI package