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Given an ExpressionSet, or a data matrix with row names corresponding
to the probe or gene IDs in an accompanying annotation package, this function
returns a data structure that can be used with the plotChrMap
function. This code is based on the Makesense method from the
geneplotter package, extended to use both the CHRLOC and CHRLOCEND
annotation environments from recent AnnotationDbi packages.
In principle, any AnnotationDbi-based package could be used to provide chromosome location data to this function; all that matters is that the probe or gene identifiers used by the annotation package should be from the same source as the data ExpressionSet featureNames or matrix row names.
makeChrStrandData(expr, lib)plotChrMap, ChrStrandData-class
data('demo')
chrdata <- makeChrStrandData(exprs(ALLs.chr22), lib = "hgu95av2.db")
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