Make chromosomalPositions dataset into a GRanges object
Issue #10
resolved
From Martin Morgan:
Your package would benefit by more closely integrating with Bioconductor data structures, especially GenomicRanges, Biostrings, and SummarizedExperiment. For instance, the data set chromosomalPositions seems to be a very natural candidate for representation as a GRanges
makeGRangesFromDataFrame(do.call(rbind, chromosomalPositions),
start.field="StartPosition", end.field="EndPosition",
keep.extra.columns=TRUE)
Consider adding functionality to also convert
WideSomaLogicData
toSummarizedExperiment
(the modern version of ExpressionSet)
I added an
as.SummarizedExperiment
method. I can't see howBiostrings
is useful to us. Use ofGenomicRanges
still to do.