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);