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

[Up] [Top]

Documentation for package ‘stageR’ version 1.10.0

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