SEAparams-class: SEAparams S4 class implementation in R

In MIGSA: Massive and Integrative Gene Set Analysis

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"
)

MIGSA documentation built on Nov. 8, 2020, 8:26 p.m.