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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
