stageR: stage-wise analysis of high throughput gene expression data in R

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Documentation for package ‘stageR’ version 1.4.0

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adjustedAlphaLevel Get adjusted significance level from the screening stage.
adjustedAlphaLevel,stageR Get adjusted significance level from the screening stage.
adjustedAlphaLevel,stageRTx Get adjusted significance level from the screening stage.
adjustedAlphaLevel-method Get adjusted significance level from the screening stage.
esetProstate Transcript-level abundance estimates in 14 Chinese prostate cancer patients
getAdjustedPValues Retrieve the stage-wise adjusted p-values.
getAdjustedPValues,stageR Retrieve the stage-wise adjusted p-values.
getAdjustedPValues,stageRTx Retrieve the stage-wise adjusted p-values.
getAdjustedPValues-method Retrieve the stage-wise adjusted p-values.
getAlpha Retrieve the significance level for the stage-wise adjustment.
getAlpha,stageR Retrieve the significance level for the stage-wise adjustment.
getAlpha,stageRTx Retrieve the significance level for the stage-wise adjustment.
getAlpha-method Retrieve the significance level for the stage-wise adjustment.
getMethod Retrieve FWER correction method.
getMethod,stageR Retrieve FWER correction method.
getMethod,stageRTx Retrieve FWER correction method.
getMethod-method Retrieve FWER correction method.
getPConfirmation Return unadjusted confirmation hypothesis p-values from a 'stageRClass' object.
getPConfirmation,stageR Return unadjusted confirmation hypothesis p-values from a 'stageRClass' object.
getPConfirmation,stageRTx Return unadjusted confirmation hypothesis p-values from a 'stageRClass' object.
getPConfirmation-method Return unadjusted confirmation hypothesis p-values from a 'stageRClass' object.
getPScreen Return screening hypothesis p-values from a 'stageRClass' object.
getPScreen,stageR Return screening hypothesis p-values from a 'stageRClass' object.
getPScreen,stageRTx Return screening hypothesis p-values from a 'stageRClass' object.
getPScreen-method Return screening hypothesis p-values from a 'stageRClass' object.
getResults Get significance results according to a stage-wise analysis.
getResults,stageR Get significance results according to a stage-wise analysis.
getResults,stageRTx Get significance results according to a stage-wise analysis.
getSignificantGenes Return significant genes when performing transcript-level analysis.
getSignificantGenes,stageRTx Return significant genes when performing transcript-level analysis.
getSignificantTx Return significant transcripts when performing transcript-level analysis.
getSignificantTx,stageR Return significant transcripts when performing transcript-level analysis.
getSignificantTx,stageRTx Return significant transcripts when performing transcript-level analysis.
getTx2gene Retrieve the data frame linking genes to transcripts.
getTx2gene,stageRTx Retrieve the data frame linking genes to transcripts.
hammer.eset Hammer dataset
isAdjusted Has stage-wise adjustment already been performed on the object?
isAdjusted,stageR Has stage-wise adjustment already been performed on the object?
isAdjusted,stageRTx Has stage-wise adjustment already been performed on the object?
isAdjusted-method Has stage-wise adjustment already been performed on the object?
isPScreenAdjusted Are the screening p-values adjusted for multiplicity?
isPScreenAdjusted,stageR Are the screening p-values adjusted for multiplicity?
isPSCreenAdjusted,stageRTx Are the screening p-values adjusted for multiplicity?
isPScreenAdjusted-method Are the screening p-values adjusted for multiplicity?
stageR Create stageR object
stageRClass The stageR class
stageRTx Create stageRTx object.
stageRTxClass The stageR class
stageWiseAdjustment adjust p-values in a two-stage analysis
stageWiseAdjustment,stageR adjust p-values in a two-stage analysis
stageWiseAdjustment,stageRTx adjust p-values in a two-stage analysis
stageWiseAdjustment-method adjust p-values in a two-stage analysis