use GDSArray to interact with bigmelon serialization as SummarizedExperiment

bm2SE.R

library(S4Vectors)
library(SummarizedExperiment)
library(GDSArray)
library(bigmelon)
data(melon)
tf = tempfile()
es2gds(melon, tf)

bm2SE = function(gdsf, elem="betas",
    fdkeep=c("ProbeID_A", "ProbeID_B", "ILMNID", "NAME",
    "GENOME_BUILD", "CHROMOSOME_36", "COORDINATE_36"),
    rnvbl = "ILMNID",
    sampnvbl = "sampleID") {
   nodes = gdsnodes(gdsf)
   pnodes = grep("pData", nodes, value=TRUE)
   stopifnot(elem %in% nodes)
   el = GDSArray::GDSArray(gdsf, elem)
# process fData
   fd = lapply(fdkeep, function(x) as.character(GDSArray::GDSArray(gdsf, paste0("fData/", x))))
   fd = DataFrame(data.frame(t(do.call(rbind, fd))))
   names(fd) = fdkeep
# process pData
   pd = lapply(pnodes, function(x) as.character(GDSArray::GDSArray(gdsf, x)))
   pd = DataFrame(data.frame(t(do.call(rbind, pd))))
   colnames(pd) = basename(pnodes)
   ans = SummarizedExperiment(assays=SimpleList(el), rowData=fd, colData=pd)
   assayNames(ans) = elem
   rownames(ans) = fd[, rnvbl]
   colnames(ans) = pd[, sampnvbl]
   ans
}

x = bm2SE(tf)  # will close and message

#> x = bm2SE("test.gds")
#                                                      FileName ReadOnly  State
#1 /Users/vincentcarey/BIOC_SOURCES/bigmelon/vignettes/test.gds    FALSE closed
#> x
#class: SummarizedExperiment
#dim: 3363 12
#metadata(0):
#assays(1): betas
#rownames(3363): cg00000029 cg00000108 ... rs966367 rs9839873
#rowData names(7): ProbeID_A ProbeID_B ... CHROMOSOME_36 COORDINATE_36
#colnames(12): 6057825008_R01C01 6057825008_R01C02 ... 6057825008_R06C01
#  6057825008_R06C02
#colData names(3): sampleID label sex
#> assay(x["rs966367",])
#<1 x 12> DelayedMatrix object of type "double":
#         6057825008_R01C01 ... 6057825008_R06C02
#rs966367           0.86588   .           0.17073