| Title: | Load and Save MultiAssayExperiments |
|---|---|
| Description: | Save MultiAssayExperiments into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties. |
| Authors: | Aaron Lun [aut, cre] |
| Maintainer: | Aaron Lun <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.5.0 |
| Built: | 2024-07-20 05:26:43 UTC |
| Source: | https://github.com/bioc/alabaster.mae |
Read a MultiAssayExperiment from its on-disk representation.
This is usually not directly called by users, but is instead called by dispatch in readObject.
readMultiAssayExperiment(path, metadata, ...)readMultiAssayExperiment(path, metadata, ...)
path |
String containing a path to a directory, itself created using the |
metadata |
Named list of metadata for this object, see |
... |
Further arguments passed to internal |
A MultiAssayExperiment object.
Aaron Lun
library(SummarizedExperiment) # Mocking up an MAE mat <- matrix(rnorm(1000), ncol=10) colnames(mat) <- letters[1:10] rownames(mat) <- sprintf("GENE_%i", seq_len(nrow(mat))) se <- SummarizedExperiment(list(counts=mat)) library(MultiAssayExperiment) mae <- MultiAssayExperiment(list(gene=se)) # Staging it: tmp <- tempfile() dir.create(tmp) info <- stageObject(mae, tmp, "dataset") # Loading it back in: loadMultiAssayExperiment(info, tmp)library(SummarizedExperiment) # Mocking up an MAE mat <- matrix(rnorm(1000), ncol=10) colnames(mat) <- letters[1:10] rownames(mat) <- sprintf("GENE_%i", seq_len(nrow(mat))) se <- SummarizedExperiment(list(counts=mat)) library(MultiAssayExperiment) mae <- MultiAssayExperiment(list(gene=se)) # Staging it: tmp <- tempfile() dir.create(tmp) info <- stageObject(mae, tmp, "dataset") # Loading it back in: loadMultiAssayExperiment(info, tmp)
Save a MultiAssayExperiment to its on-disk representation.
## S4 method for signature 'MultiAssayExperiment' saveObject(x, path, ...)## S4 method for signature 'MultiAssayExperiment' saveObject(x, path, ...)
x |
A MultiAssayExperiment object or one of its subclasses. |
path |
String containing the path to a directory in which to save |
... |
Further arguments to pass to specific methods. |
The contents of x are saved into a path, and NULL is invisibly returned.
Aaron Lun
# Mocking up an MAE mat <- matrix(rnorm(1000), ncol=10) colnames(mat) <- letters[1:10] rownames(mat) <- sprintf("GENE_%i", seq_len(nrow(mat))) library(SummarizedExperiment) se <- SummarizedExperiment(list(counts=mat)) library(MultiAssayExperiment) mae <- MultiAssayExperiment(list(gene=se)) # Saving it: tmp <- tempfile() saveObject(mae, tmp)# Mocking up an MAE mat <- matrix(rnorm(1000), ncol=10) colnames(mat) <- letters[1:10] rownames(mat) <- sprintf("GENE_%i", seq_len(nrow(mat))) library(SummarizedExperiment) se <- SummarizedExperiment(list(counts=mat)) library(MultiAssayExperiment) mae <- MultiAssayExperiment(list(gene=se)) # Saving it: tmp <- tempfile() saveObject(mae, tmp)