ExprData-class: ExprData S4 class implementation in R

In MIGSA: Massive and Integrative Gene Set Analysis

Description

This S4 class contains the expression data, it can be a MAList or DGEList. Important: Rownames are going to be used as gene identifiers, make sure that this IDs are the same used in your gene sets.

Examples

## Lets create a ExprData object from counts data (DGEList).
rnaData <- matrix(rnbinom(10000, mu = 5, size = 2), ncol = 4)
rownames(rnaData) <- 1:nrow(rnaData)
# It must have rownames (gene names).

## Now we can use rnaExprData as an ExprData object.
## Not run: 
rnaExprData <- DGEList(counts = rnaData)

## End(Not run)

## Lets create a ExprData object from micro array data (MAList).
maData <- matrix(rnorm(10000), ncol = 4)
rownames(maData) <- 1:nrow(maData)
# It must have rownames (gene names).

## Now we can use maExprData as an ExprData object.
maExprData <- new("MAList", list(M = maData))

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