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

## Documentation for package ‘stageR’ version 1.9.0

- 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