pumaFull {puma} | R Documentation

## Perform a full PUMA analysis

### Description

Full analysis including pumaPCA and mmgmos/pumaDE vs rma/limma comparison

### Usage

    pumaFull (
    	ExpressionFeatureSet = NULL
    ,	data_dir = getwd()
    ,	load_ExpressionFeatureSet = FALSE
    ,	calculate_eset = TRUE
    ,	calculate_pumaPCAs = TRUE
    ,	calculate_bcomb = TRUE
    ,	mmgmosComparisons = FALSE
    )

### Arguments

`ExpressionFeatureSet` | An object of class `FeatureSet`.
`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 `data_dir` directory.
`calculate_eset` | Boolean. Calculate ExpressionSet from `ExpressionFeatureSet` object? If FALSE, files named "eset\_mmgmos.rda" and "eset\_rma.rda" must be available in the `data\_dir` directory.
`calculate_pumaPCAs` | Boolean. Calculate pumaPCA from `eset\_mmgmos` object? If FALSE, a file named "pumaPCA\_results.rda" must be available in the `data\_dir` directory.
`calculate_bcomb` | Boolean. Calculate pumaComb from `eset\_mmgmos` object? If FALSE, files named "eset\_comb.rda" and "eset\_normd\_comb.rda" must be available in the `data\_dir` directory.
`mmgmosComparisons` | Boolean. If TRUE, will compare mmgmos with default settings, with mmgmos used with background correction.

### Value

No return values. Various objects are saved as .rda files during the execution of this function, and various PDF files are created.

### Author(s)

Richard D. Pearson

### See Also

Related methods `pumaDE`, `createDesignMatrix` and `createContrastMatrix`

### Examples

    ##	Code commented out to ensure checks run quickly
    #	if (require(pumadata)) data(oligo.estrogen)
    #	pumaFull(oligo.estrogen)

[Package puma version 3.22.0 Index]