eset_to_matrix: Convert a 'Biobase::ExpressionSet' to a gene-expression...

In federicomarini/quantiseqr: Quantification of the Tumor Immune contexture from RNA-seq data

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"))

federicomarini/quantiseqr documentation built on May 7, 2024, 9:50 a.m.