eset_to_matrix {quantiseqr}

R Documentation

Convert a Biobase::ExpressionSet to a gene-expression matrix.

Description

Convert a Biobase::ExpressionSet to a gene-expression matrix.

Usage

eset_to_matrix(eset, column)

Arguments

eset	ExpressionSet
column	column name of the fData() table, which contains the HGNC gene symbols.

Value

A matrix with gene symbols as rownames and sample identifiers as colnames.

Examples

data(dataset_racle)
dim(dataset_racle$expr_mat)

library("Biobase")
es_racle <- ExpressionSet(assayData = dataset_racle$expr_mat)
featureData(es_racle)$gene_symbol <- rownames(dataset_racle$expr_mat)

es_racle

head(eset_to_matrix(es_racle, "gene_symbol"))

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