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.
Martin
Sean
On Sat, Sep 20, 2014 at 10:38 AM, Vincent Carey <st...@channing.harvard.edu>
wrote:
do we have a facility for this?
if not, we have
https://github.com/vjcitn/biocMultiAssay/blob/master/R/exs2se.R
https://github.com/vjcitn/biocMultiAssay/blob/master/man/coerce-methods.Rd
it occurred to me that we might want something like this in GenomicRanges
(that's where SummarizedExperiment is managed, right?) and I will add it
if there are no objections
the arguments are currently
assayname = "exprs", # for naming SimpleList element
fngetter =
function(z) rownames(exprs(z)), # extract usable feature names
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 duplicated
features
if (any(isd <- duplicated(z[,"PROBEID"])))
return(z[!isd,,drop=FALSE])
z
},
signIsStrand = TRUE, # verify that signs of addresses define strand
ucsdChrnames = TRUE # prefix 'chr' to chromosome token
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