Biobase::ExpressionSet to a gene-expression matrix.eset_to_matrix.RdConvert a Biobase::ExpressionSet to a gene-expression matrix.
eset_to_matrix(eset, column)ExpressionSet
column name of the fData() table, which contains the HGNC gene symbols.
A matrix with gene symbols as rownames and sample identifiers as colnames.
data(dataset_racle)
dim(dataset_racle$expr_mat)
#> [1] 32467 4
library("Biobase")
#> Loading required package: BiocGenerics
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#> Attaching package: ‘BiocGenerics’
#> The following objects are masked from ‘package:stats’:
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#> IQR, mad, sd, var, xtabs
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#> lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#> pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
#> union, unique, unsplit, which.max, which.min
#> Welcome to Bioconductor
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#> Vignettes contain introductory material; view with
#> 'browseVignettes()'. To cite Bioconductor, see
#> 'citation("Biobase")', and for packages 'citation("pkgname")'.
es_racle <- ExpressionSet(assayData = dataset_racle$expr_mat)
featureData(es_racle)$gene_symbol <- rownames(dataset_racle$expr_mat)
es_racle
#> ExpressionSet (storageMode: lockedEnvironment)
#> assayData: 32467 features, 4 samples
#> element names: exprs
#> protocolData: none
#> phenoData: none
#> featureData
#> featureNames: A1BG A1CF ... ZZEF1 (32467 total)
#> fvarLabels: gene_symbol
#> fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> Annotation:
head(eset_to_matrix(es_racle, "gene_symbol"))
#> LAU125 LAU355 LAU1255 LAU1314
#> A1BG 0.82 0.58 0.81 0.71
#> A1CF 0.00 0.01 0.00 0.00
#> A2M 247.15 24.88 2307.94 20.30
#> A2M-AS1 1.38 0.20 2.60 0.28
#> A2ML1 0.03 0.00 0.05 0.02
#> A3GALT2 0.00 0.00 0.00 0.00