pumaFull {puma} | R Documentation |
Full analysis including pumaPCA and mmgmos/pumaDE vs rma/limma comparison
pumaFull ( ExpressionFeatureSet = NULL , data_dir = getwd() , load_ExpressionFeatureSet = FALSE , calculate_eset = TRUE , calculate_pumaPCAs = TRUE , calculate_bcomb = TRUE , mmgmosComparisons = FALSE )
ExpressionFeatureSet |
An object of class |
data_dir |
A character string specifying where data files are stored. |
load_ExpressionFeatureSet |
Boolean. Load a pre-existing ExpressionFeatureSet object? Note that this has to be named "ExpressionFeatureSet.rda" and be in the |
calculate_eset |
Boolean. Calculate ExpressionSet from |
calculate_pumaPCAs |
Boolean. Calculate pumaPCA from |
calculate_bcomb |
Boolean. Calculate pumaComb from |
mmgmosComparisons |
Boolean. If TRUE, will compare mmgmos with default settings, with mmgmos used with background correction. |
No return values. Various objects are saved as .rda files during the execution of this function, and various PDF files are created.
Richard D. Pearson
Related methods pumaDE
, createDesignMatrix
and createContrastMatrix
## Code commented out to ensure checks run quickly # if (require(pumadata)) data(oligo.estrogen) # pumaFull(oligo.estrogen)