SingleCellMultiModal: Combining Modalities into one MultiAssayExperiment

In waldronlab/SingleCellMultiModal: Integrating Multi-modal Single Cell Experiment datasets

Combining Modalities into one MultiAssayExperiment

Description

Combine multiple single cell modalities into one using the input of the individual functions.

Usage

SingleCellMultiModal(
  DataTypes,
  modes = "*",
  versions = "1.0.0",
  dry.run = TRUE,
  verbose = TRUE,
  ...
)

Arguments

DataTypes	character() A vector of data types as indicated in each individual function by the DataType parameter. These can be any of the following: "mouse_gastrulation", "pbmc_10x", "macrophage_differentiation", "cord_blood", "peripheral_blood", "mouse_visual_cortex", "mouse_embryo_8_cell"
modes	list() A list or CharacterList of modes for each data type where each element corresponds to one data type.
versions	character() A vector of versions for each DataType. By default, version ⁠1.0.0⁠ is obtained for all data types.
dry.run	logical(1) Whether to return the dataset names before actual download (default TRUE)
verbose	logical(1) Whether to show the dataset currently being (down)loaded (default TRUE)
...	Additional arguments passed on to the ExperimentHub-class constructor

Value

A multi-modality MultiAssayExperiment

metadata

The metadata in the MultiAssayExperiment contains the original function call used to generate the object (labeled as call), a call_map which provides traceability of technology functions to DataType prefixes, and lastly, R version information as version.

Examples

SingleCellMultiModal(c("mouse_gastrulation", "pbmc_10x"),
    modes = list(c("acc*", "met*"), "rna"),
    version = c("2.0.0", "1.0.0"), dry.run = TRUE, verbose = TRUE
)

waldronlab/SingleCellMultiModal documentation built on Nov. 3, 2024, 7:32 p.m.