Save a TreeSummarizedExperiment to disk

Save a TreeSummarizedExperiment to its on-disk representation.

Usage

# S4 method for class 'TreeSummarizedExperiment'
saveObject(x, path, ...)

Arguments

x

A TreeSummarizedExperiment object or one of its subclasses.

path

String containing the path to a directory in which to save x.

...

Further arguments to pass to "saveObject,SingleCellExperiment-method".

Value

x is saved into path and NULL is invisibly returned.

Details

Everything inherited from the SingleCellExperiment parent class is saved by alabaster.sce. The TreeSummarizedExperiment-specific slots are saved as follows:

• Each tree in rowTree or colTree is saved as a list containing the fields of the phylo object, where the edge matrix is split into parent and child vectors. This preserves the node numbering and arbitrary tip/node labels, which would not survive a round trip through Newick.

• rowLinks and colLinks are saved as data frames.

• referenceSeq is saved as FASTA via alabaster.string. A DNAStringSetList is saved as a list of such sequence sets.

See also

readTreeSummarizedExperiment, to read the TreeSummarizedExperiment back into the R session.

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)
list.files(tmp, recursive = TRUE)
#>  [1] "OBJECT"                                
#>  [2] "_environment.json"                     
#>  [3] "assays/0/OBJECT"                       
#>  [4] "assays/0/array.h5"                     
#>  [5] "assays/names.json"                     
#>  [6] "column_data/OBJECT"                    
#>  [7] "column_data/basic_columns.h5"          
#>  [8] "reference_sequences/OBJECT"            
#>  [9] "reference_sequences/names.txt.gz"      
#> [10] "reference_sequences/sequences.fasta.gz"
#> [11] "row_data/OBJECT"                       
#> [12] "row_data/basic_columns.h5"             
#> [13] "row_links/OBJECT"                      
#> [14] "row_links/basic_columns.h5"            
#> [15] "row_trees/0/OBJECT"                    
#> [16] "row_trees/0/list_contents.h5"          
#> [17] "row_trees/names.json"