inst/extdata/loadMultiAssayExperiment.R

In trichelab/enmity: load scNMT data and test HDF5/DelayedArray/restfulSE behavior

# BiocManager::install("trichelab/enmity")
library(enmity) 
library(HDF5Array)
library(MultiAssayExperiment) 

if (!exists("meth_hdf5")) meth_hdf5 <-loadHDF5SummarizedExperiment("scNMT_meth")
if (!exists("acc_hdf5")) acc_hdf5 <- loadHDF5SummarizedExperiment("scNMT_acc")
if (!exists("rna_hdf5")) rna_hdf5 <- loadHDF5SummarizedExperiment("scNMT_rna")

assayList <- list(meth = meth_hdf5, acc = acc_hdf5, rna = rna_hdf5)
ExpList <- ExperimentList(assayList)

commonColDat <- Reduce(intersect, 
                       lapply(ExpList, function(x) names(colData(x))))
colDat <- DataFrame(do.call(cbind, 
                            lapply(ExpList, 
                                   function(x) colData(x)[[commonColDat]])))

# this gets tricky because there are 8 misses
rownames(colDat) <- apply(colDat, 1, LCS)

# sample mappings: 
maplist <- apply(colDat, 2, 
                 function(x) DataFrame(primary=names(x), colname=x))
sampMap <- listToMap(maplist)

# disambiguate the column names for the main MAE:
names(colDat) <- paste(commonColDat, names(colDat), sep=".") 

# assemble the MultiAssayExperiment:
scNMT <- MultiAssayExperiment(experiments = ExpList,
                              colData = colDat, 
                              sampleMap = sampMap)

# save it
saveRDS(scNMT, file="scNMT.rds")