a4 (version 1.20.0)

createExpressionSet: combine gene expression and phenotype data onto a ExpressionSet object

Description

Basically a wrapper for new('ExpressionSet',...), this function gathers gene expression and phenotype data, after having checked their compatibility.

Usage

createExpressionSet(exprs = new("matrix"), phenoData = new("AnnotatedDataFrame"), varMetadata = NULL, dimLabels = c("rowNames", "colNames"), featureData = NULL, experimentData = new("MIAME"), annotation = character(0), changeColumnsNames = TRUE, ...)

Arguments

exprs

gene expression matrix

phenoData

phenotype data associated with exprs columns, as a matrix or data.frame

varMetadata

optional metadata on phenotype data

dimLabels

see 'ExpressionSet'

featureData

see 'ExpressionSet'

experimentData

see 'ExpressionSet'

annotation

see 'ExpressionSet'

changeColumnsNames

Change exprs columns names -- see details

...

...

Value

• An object of class ExpressionSet

Details

If changeColumnsNames is TRUE, then the procedure is the following: first one checks if phenoData contains a column named 'colNames'. If so, content will be used to rename exprs colums. On the other case, one uses combinations of phenoData columns to create new names. In any case, old columns names are stored within a column named 'oldcolnames' in the pData.

See Also

ExpressionSet

Examples

# simulate expression data of 10 features (genes) measured in 4 samples
x <- matrix(rnorm(40), ncol = 4)
colnames(x) <- paste("sample", 1:4, sep = "_")
rownames(x) <- paste("feature", 1:10, sep = "_")

# simulate a phenodata with two variables
ToBePheno <- data.frame(Gender = rep(c('Male','Female'), 2), 
		Treatment = rep(c('Trt','Control'), each=2))
rownames(ToBePheno) <- paste("sample", 1:4, sep = "_")

eset <- createExpressionSet(exprs = x, phenoData = ToBePheno)