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


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Documentation for package ‘stageR’ version 1.0.0

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