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

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Documentation for package ‘stageR’ version 1.27.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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