geneChip Analysis Package

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Documentation for package ‘ArrayTools’ version 1.40.0

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A C D E G H I M O P Q R S

-- A --

adjustment Access the multiple comparison adjustment method from the regressResult or interactionResult class
adjustment-method Class to Contain the Regression Result Based on An Interaction Model
adjustment-method Class to Contain the Regression Result

-- C --

class:contrastMatrix Class to Contain the Contrast Matrix that Used for Linear Regression
class:designMatrix Class to Contain the Design Matrix that Used for Linear Regression
class:interactionResult Class to Contain the Regression Result Based on An Interaction Model
class:regressResult Class to Contain the Regression Result
contrastMatrix Class to Contain the Contrast Matrix that Used for Linear Regression
contrastMatrix-class Class to Contain the Contrast Matrix that Used for Linear Regression
createExpressionSet Creating an ExpressionSet
createGSEAFiles A Wrapper Function to create *.GCT and *.CLS for GSEA analysis
createIndex Creating an HTML index file
createIngenuityFile A Wrapper Function to Create Files for Ingenuity Analysis

-- D --

designMatrix Class to Contain the Design Matrix that Used for Linear Regression
designMatrix-class Class to Contain the Design Matrix that Used for Linear Regression

-- E --

eSetExample An ExpressionSet example
exprsExample a data.frame contains expression data

-- G --

geneFilter filter an ExpressionSet using different methods
getAdjP access the adjPVal slot from regressResult or interactionResult class
getAdjP-method Class to Contain the Regression Result Based on An Interaction Model
getAdjP-method Class to Contain the Regression Result
getAnnotation access the annotation slot from the regressResult or interactionResult slot
getAnnotation-method Class to Contain the Regression Result Based on An Interaction Model
getAnnotation-method Class to Contain the Regression Result
getCompare1 Access the Compare1 slot from the contrastMatrix
getCompare1-method Class to Contain the Contrast Matrix that Used for Linear Regression
getCompare2 Access the compare2 slot from the contrastMatrix class
getCompare2-method Class to Contain the Contrast Matrix that Used for Linear Regression
getContrast Access the contrast matrix from the contrastMatrix class
getContrast-method Class to Contain the Contrast Matrix that Used for Linear Regression
getContrast-method Class to Contain the Regression Result Based on An Interaction Model
getContrast-method Class to Contain the Regression Result
getCovariates Accessing the covariates from the designMatrix class
getCovariates-method Class to Contain the Design Matrix that Used for Linear Regression
getDesign Access the design matrix from the designMatrix class
getDesign-method Class to Contain the Design Matrix that Used for Linear Regression
getF access the foldChange slot from regressionResult or interactionResult class
getF-method Class to Contain the Regression Result Based on An Interaction Model
getF-method Class to Contain the Regression Result
getFC Access the foldChange slot from the regressResult or interactionResult class
getFC-method Class to Contain the Regression Result Based on An Interaction Model
getFC-method Class to Contain the Regression Result
getFCCutoff Access the significantFCCutoff slot from the regressResult or interactionResult class
getFCCutoff-method Class to Contain the Regression Result Based on An Interaction Model
getFCCutoff-method Class to Contain the Regression Result
getFileName-method Class to Contain the Regression Result Based on An Interaction Model
getFileName-method Class to Contain the Regression Result
getFilterMethod Access the filterMethod slot from the regressResult or interactionResult class
getFilterMethod-method Class to Contain the Regression Result Based on An Interaction Model
getFilterMethod-method Class to Contain the Regression Result
getID access the ID slot from the regressResult or interactionResult class
getID-method Class to Contain the Regression Result Based on An Interaction Model
getID-method Class to Contain the Regression Result
getIndex Access the SignificantIndex slot from the regressResult or interactionResult class
getIndex-method Class to Contain the Regression Result Based on An Interaction Model
getIndex-method Class to Contain the Regression Result
getInteraction Access the interaction slot from the contrastMatrix class
getInteraction-method Class to Contain the Contrast Matrix that Used for Linear Regression
getIntIndex Access the IntIndex slot from the designMatrix class
getIntIndex-method Class to Contain the Design Matrix that Used for Linear Regression
getLength Calculate the Length of interactionResult class
getLength-method Class to Contain the Regression Result Based on An Interaction Model
getLevel Access the level slot from the contrastMatrix class
getLevel-method Class to Contain the Contrast Matrix that Used for Linear Regression
getNormalizationMethod Access the significantIndex slot from the regressResult or interactionResult class
getNormalizationMethod-method Class to Contain the Regression Result Based on An Interaction Model
getNormalizationMethod-method Class to Contain the Regression Result
getP Access the pValue slot from regressResult or interactionResult class
getP-method Class to Contain the Regression Result Based on An Interaction Model
getP-method Class to Contain the Regression Result
getPCutoff Access the significantPvalueCutoff slot from regressResult or interactionResult class
getPCutoff-method Class to Contain the Regression Result Based on An Interaction Model
getPCutoff-method Class to Contain the Regression Result
getTarget Access the target slots from the designMatrix class
getTarget-method Class to Contain the Design Matrix that Used for Linear Regression

-- H --

hugene10stCONTROL hugene10stCONTROL

-- I --

initialize-method Class to Contain the Contrast Matrix that Used for Linear Regression
initialize-method Class to Contain the Design Matrix that Used for Linear Regression
interactionResult Class to Contain the Regression Result Based on An Interaction Model
interactionResult-class Class to Contain the Regression Result Based on An Interaction Model

-- M --

mogene10stCONTROL mogene10stCONTROL

-- O --

output.cls Create *.CLS file for GSEA analysis
output.gct Create an *.GCT file for GSEA analysis
output.ing Create an Ingenuity File for Ingenuity Analysis
Output2HTML Creating HTML file for regressResult or interactionResult class
Output2HTML-method Class to Contain the Regression Result Based on An Interaction Model
Output2HTML-method Class to Contain the Regression Result

-- P --

pDataExample a phenoData example
postInteraction Create an Object of InteractionResult Class for Testing Interaction
preProcess3prime A wrapper function to normalize the the 3 prime array
preProcessGeneST Proprocess genechip ST array

-- Q --

qa3prime Creating Quality Assessment Report for 3 Prime Array
qaGeneST Creating Quality Assessment Report for Gene ST Array
QC sample QC result from Affy Expression Console

-- R --

regress Run regression to fit genewise linear model
regressionMethod Access the regressionMethod slot from the regressResult or interactionResult class
regressionMethod-method Class to Contain the Regression Result Based on An Interaction Model
regressionMethod-method Class to Contain the Regression Result
regressResult Class to Contain the Regression Result
regressResult-class Class to Contain the Regression Result

-- S --

selectSigGene select differentially expressed genes from the regressResult class
selectSigGene-method Class to Contain the Regression Result Based on An Interaction Model
selectSigGene-method Class to Contain the Regression Result
selectSigGeneInt select differentially expressed genes from the interactionResult class
show-method Class to Contain the Contrast Matrix that Used for Linear Regression
show-method Class to Contain the Design Matrix that Used for Linear Regression
show-method Class to Contain the Regression Result Based on An Interaction Model
show-method Class to Contain the Regression Result
Sort Sort a regressionResult or an interactionResult
Sort-method Class to Contain the Regression Result Based on An Interaction Model
Sort-method Class to Contain the Regression Result
summary-method Class to Contain the Regression Result Based on An Interaction Model
summary-method Class to Contain the Regression Result