createExpressionSet: combine gene expression and phenotype data onto a...

In a4Base: Automated Affymetrix Array Analysis Base Package

Description

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

Usage

createExpressionSet(
  exprs = matrix(nrow = 0, ncol = 0),
  phenoData = AnnotatedDataFrame(),
  varMetadata = NULL,
  dimLabels = c("rowNames", "colNames"),
  featureData = NULL,
  experimentData = 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
...	...

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.

Value

An object of class ExpressionSet

Author(s)

Eric Lecoutre

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)

a4Base documentation built on Nov. 8, 2020, 5:41 p.m.