SEAparams-class {MIGSA} | R Documentation

## SEAparams S4 class implementation in R

### Description

This S4 class contains the parameters to provide for SEA.

### Slots

`treat_lfc`

  numeric, lfc parameter passed to `treat` function (default: 0).

`de_cutoff`

  numeric, cutoff value to define a gene as differentialy expressed (default: 0.01).

`adjust_method`

  character, method parameter passed to `p.adjust` function (default: "fdr").

`de_genes`

  (optional) character vector of differentialy expressed genes, if not provided it will be filled using the other parameters.

`br`

  background reference to use, there are two possible options for this slot (default: "briii"):

  - character indicating to use "bri" or "briii".

  - character vector indicating the genes to use as background reference.

`test`

  character indicating which test to use, it must be one of "FisherTest", "HypergeoTest" or "BinomialTest" (default: "FisherTest").

### See Also

`GSEAparams-class`

`summary`

### Examples

    ## Lets create the default SEAparams object.
    mySeaParams <- SEAparams()
    ## Lets create another SEAparams object with my default br genes. Make sure
    ## these genes are present in the analyzed expression matrix rownames.
    myBr <- as.character(1:10)
    mySeaParamsOwnBr <- SEAparams(br = myBr)
    ## Lets create another SEAparams object with my default differentialy
    ## expressed genes. Make sure these genes are present in the analyzed
    ## expression matrix rownames.
    myDEGenes <- as.character(3:15)
    mySeaParamsOwnDEG <- SEAparams(de_genes = myDEGenes)
    ## Lets create another SEAparams object changing the differentialy
    ## expressed genes parameters.
    mySeaParamsOwnParams <- SEAparams(
      treat_lfc = 0.25, de_cutoff = 0.05,
      adjust_method = "none"
    )

[Package MIGSA version 1.11.7 Index]