| makeSummarizedExperimentFromExpressionSet {GenomicRanges} | R Documentation |
makeSummarizedExperimentFromExpressionSet takes a
ExpressionSet object as input and a Range mapping function
that maps the features to ranges. It then returns a
SummarizedExperiment object.
makeSummarizedExperimentFromExpressionSet(from,
mapFun=naiveRangeMapper)
from |
An ExpressionSet object. |
mapFun |
A function which takes an ExpressionSet object and returns a GRanges, or GRangesList object which corresponds to the genomic ranges used in the ExpressionSet. The rownames of the returned GRanges are used to match the featureNames of the ExpressionSet. naiveRangeMapper. |
A SummarizedExperiment object that corresponds to the input.
naiveRangeMapper, probeRangeMapper, geneRangeMapper
library(Biobase)
data(sample.ExpressionSet, package = "Biobase")
# using the naive coercion
makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet)
# using probe range mapper
makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet, probeRangeMapper)
# using the gene range mapper
makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet,
geneRangeMapper("TxDb.Hsapiens.UCSC.hg19.knownGene"))