On Sep 20, 2014 2:15 PM, "Martin Morgan" <mtmorgan at fhcrc.org> wrote:
On 09/20/2014 10:43 AM, Sean Davis wrote:
Hi, Vince.
Looks like a good start. I'd probably pull all the assays from
ExpressionSet into SummarizedExperiment as the default, avoiding data
coercion methods that are unnecessarily lossy. Also, as it stands, the
assayname argument is not used anyway?
I think there will be some resistance to uniting the 'Biobase' and
'IRanges' realms under 'GenomicRanges'; considerable effort has gone in to
making a rational hierarchy of package dependencies [perhaps Herve will
point to some of his ASCII art on the subject].
I have some recollection of (recent) discussion related to this topic in
the DESeq2 realm, but am drawing a blank; presumably Michael or Wolfgang or
... will chime in.
Andrzej was working on a conversion function for DESeqDataSet <=>
DGEList. I don't think it was for SummarizedExperiment and eSet.
Mike
Sean
On Sat, Sep 20, 2014 at 10:38 AM, Vincent Carey <
stvjc at channing.harvard.edu>
it occurred to me that we might want something like this in
(that's where SummarizedExperiment is managed, right?) and I will add
if there are no objections
the arguments are currently
assayname = "exprs", # for naming SimpleList element
fngetter =
function(z) rownames(exprs(z)), # extract usable feature
annDbGetter =
function(z) {
clnanno = sub(".db", "", annotation(z))
stopifnot(require(paste0(annotation(z), ".db"),
character.only=TRUE) )
get(paste0(annotation(z), ".db")) # obtain resource for
mapping feature names to coordinates
},
probekeytype = "PROBEID", # chipDb field to use
duphandler = function(z) { # action to take to process
features
if (any(isd <- duplicated(z[,"PROBEID"])))
return(z[!isd,,drop=FALSE])
z
},
signIsStrand = TRUE, # verify that signs of addresses define
ucsdChrnames = TRUE # prefix 'chr' to chromosome token
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