just for those who were interested, here is what I bolted together a LONG
time ago
warning: this will probably burn your retinas with its badness. also, no
refclasses for colData that pertains across the child SummarizedExperiments
(doh)
require(GenomicRanges) ## ensure that SummarizedExperiment has been declared
setClassUnion("SummarizedExperimentOrNULL",c("SummarizedExperiment","NULL"))
## slots: exprData, methData, geneData, exonData, lincData, mirData, cnvData
setClass("MergedDataSet", contains=c("eSet"), # {{{
representation=representation(
exprData="SummarizedExperimentOrNULL", # exprs, pvals?
methData="SummarizedExperimentOrNULL", # betas, totals
geneData="SummarizedExperimentOrNULL", # counts, RPKM, pvals?
exonData="SummarizedExperimentOrNULL", # counts, RPKM
lincData="SummarizedExperimentOrNULL", # counts, RPKM
mirData="SummarizedExperimentOrNULL", # counts, RPKM
cnvData="SummarizedExperimentOrNULL" # RLE CN, pvals?
)) # }}}
setValidity("MergedDataSet", function(object) { # {{{ check sample names
valid = TRUE
genome = NULL
samples = NULL
for( s in c('exprData', 'methData', 'geneData',
'exonData', 'lincData', 'mirData', 'cnvData') ) {
if( !empty(slot(object, s)) ) {
# do all of the genomes match?
if(is(slot(object, s), 'SummarizedExperiment')) {
if(is.null(genome)) genome = unique(genome(slot(object, s)))
valid = valid && (genome == unique(genome(slot(object, s))))
}
# do all of the samples match?
if(is(slot(object, s), 'ExpressionSet')) {
samples.s = sampleNames(slot(object, s))
} else if(is(slot(object, s), 'SummarizedExperiment')) {
samples.s = colnames(slot(object, s))
}
if(is.null(samples)) samples = samples.s
valid = valid && (samples == samples.s)
}
}
return( valid )
}) # }}}
setMethod("show",signature(object="MergedDataSet"), function(object) { #
{{{
callNextMethod()
available = c()
for( s in c('exprData', 'methData', 'geneData',
'exonData', 'lincData', 'mirData', 'cnvData') ) {
if(!empty(slot(object, s))) available = append(available, s)
}
if(empty(available)) cat('No experimental data has been added yet.\n')
else cat('Available data types:\n', paste(available, collapse=', '), '\n')
message("FIXME: add methods to automatically add columns of NAs to new
data")
}) # }}}
--
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
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