Combining Modalities into one MultiAssayExperiment — SingleCellMultiModal • SingleCellMultiModal

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
)
#> Running scNMT...
#> Running scMultiome...
#> $mouse_gastrulation
#>     ah_id         mode file_size rdataclass rdatadateadded rdatadateremoved
#> 1  EH3753      acc_cgi   21.1 Mb     matrix     2020-09-03             <NA>
#> 2  EH3754     acc_CTCF    1.2 Mb     matrix     2020-09-03             <NA>
#> 3  EH3755      acc_DHS   16.2 Mb     matrix     2020-09-03             <NA>
#> 4  EH3756 acc_genebody   60.1 Mb     matrix     2020-09-03             <NA>
#> 5  EH3757     acc_p300    0.2 Mb     matrix     2020-09-03             <NA>
#> 6  EH3758 acc_promoter   33.8 Mb     matrix     2020-09-03             <NA>
#> 7  EH3760      met_cgi   12.1 Mb     matrix     2020-09-03             <NA>
#> 8  EH3761     met_CTCF    0.1 Mb     matrix     2020-09-03             <NA>
#> 9  EH3762      met_DHS    3.9 Mb     matrix     2020-09-03             <NA>
#> 10 EH3763 met_genebody   33.9 Mb     matrix     2020-09-03             <NA>
#> 11 EH3764     met_p300    0.1 Mb     matrix     2020-09-03             <NA>
#> 12 EH3765 met_promoter   18.7 Mb     matrix     2020-09-03             <NA>
#> 
#> $pbmc_10x
#>    ah_id   mode file_size           rdataclass rdatadateadded rdatadateremoved
#> 1 EH6689 rna_se    0.6 Mb SingleCellExperiment     2021-07-16             <NA>
#> 2 EH4629    rna   57.7 Mb            dgCMatrix     2020-09-24             <NA>
#>