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.


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Documentation for package ‘oneChannelGUI’ version 1.6.5

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

-- --

oneChannelGUI-package Set of functions extending the capability of affylmGUI 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
crosshybhuex10stv2na23hg18 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
crosshybmoex10stv1na23mm8 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
crosshybraex10stv1na23rn4 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
huex10stv2na23hg18 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
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
moex10stv1na23mm8 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
raex10stv1na23rn4 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
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

-- V --

VennDiagram Venn diagrams using two or three lists

-- W --

whichKindOfArray Starting oneChannelGUI package