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 1.4.0 Index]