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"))