IGSAinput-class {MIGSA} | R Documentation

## IGSAinput S4 class implementation in R

### Description

This S4 class contains all the necessary inputs to execute a functional analysis (SEA and GSEA) on one experiment. Important: Make sure that gene IDs are concordant between the expression matrix and the provided gene sets.

### Slots

`name`

  character indicating the name of this experiment.

`expr_data`

  ExprData object with the expression data (MicroArray or RNAseq). Note: expr_data can be a 0x0 matrix only if gsea_params=NULL and de_genes and br slots from sea_params are correctly set (vectors of gene names), in this case only SEA will be run.

`fit_options`

  FitOptions object with the parameters to be used when fitting the model.

`gene_sets_list`

  named list of GeneSetCollection objects to be tested for enrichment (names must be unique).

`sea_params`

  SEAparams object with the parameters to be used by SEA, if NULL then SEA wont be run.

`gsea_params`

  GSEAparams object with the parameters to be used by GSEA, if NULL then GSEA wont be run.

### See Also

`ExprData-class`

`SEAparams-class`

`GSEAparams-class`

`IGSAinput-getterSetters`

`getDEGenes`

`MIGSA`

`summary`

### Examples

    ## Lets create a basic IGSAinput object.
    ## First create a expression matrix.
    maData <- matrix(rnorm(10000), ncol = 4)
    rownames(maData) <- 1:nrow(maData)
    # It must have rownames (gene names).
    maExprData <- new("MAList", list(M = maData))
    ## Now lets create the FitOptions object.
    myFOpts <- FitOptions(c("Cond1", "Cond1", "Cond2", "Cond2"))
    ## Finally lets create the Genesets to test for enrichment.
    library(GSEABase)
    myGs1 <- GeneSet(as.character(1:10),
      setIdentifier = "fakeId1",
      setName = "fakeName1"
    )
    myGs2 <- GeneSet(as.character(7:15),
      setIdentifier = "fakeId2",
      setName = "fakeName2"
    )
    myGSs <- GeneSetCollection(list(myGs1, myGs2))
    ## And now we can create our IGSAinput ready for MIGSA.
    igsaInput <- IGSAinput(
      name = "igsaInput", expr_data = maExprData,
      fit_options = myFOpts, gene_sets_list = list(myGSs = myGSs)
    )
    ## Valid IGSAinput object with no expr_data (only run SEA).
    igsaInput <- IGSAinput(
      name = "igsaInput", gene_sets_list = list(myGSs = myGSs),
      gsea_params = NULL,
      sea_params = SEAparams(
        de_genes = rownames(maExprData)[1:10],
        br = rownames(maExprData)
      )
    )
    validObject(igsaInput)

[Package MIGSA version 1.12.0 Index]