Read a TreeSummarizedExperiment from disk

Read a TreeSummarizedExperiment object from its on-disk representation. This is usually not directly called by users, but is instead called by dispatch in readObject.

Usage

readTreeSummarizedExperiment(path, metadata, ...)

Arguments

path

String containing a path to a directory, itself created using the saveObject method for TreeSummarizedExperiment objects.

metadata

Named list of metadata for this object, see readObjectFile for details.

...

Further arguments passed to readSingleCellExperiment and internal altReadObject calls.

Value

A TreeSummarizedExperiment object.

See also

"saveObject,TreeSummarizedExperiment-method", to save the TreeSummarizedExperiment to disk.

Examples

# Mocking up a TreeSE:
data(tinyTree, package = "TreeSummarizedExperiment")
mat <- matrix(rpois(100, 10), ncol = 10)
rownames(mat) <- tinyTree[["tip.label"]]
colnames(mat) <- letters[1:10]

tse <- TreeSummarizedExperiment(list(counts = mat), rowTree = tinyTree)
tse[["stuff"]] <- LETTERS[1:10]
referenceSeq(tse) <- Biostrings::DNAStringSet(rep("ACGT", nrow(tse)))

# Staging it:
tmp <- tempfile()
saveObject(tse, tmp)
readObject(tmp)
#> class: TreeSummarizedExperiment 
#> dim: 10 10 
#> metadata(0):
#> assays(1): counts
#> rownames(10): t2 t7 ... t5 t3
#> rowData names(0):
#> colnames(10): a b ... i j
#> colData names(1): stuff
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> rowLinks: a LinkDataFrame (10 rows)
#> rowTree: 1 phylo tree(s) (10 leaves)
#> colLinks: NULL
#> colTree: NULL
#> referenceSeq: a DNAStringSet (10 sequences)