Single-cell Multiome ATAC + Gene Expression

10x Genomics Multiome technology enables simultaneous profiling of the transcriptome (using 3’ gene expression) and epigenome (using ATAC-seq) from single cells to deepen our understanding of how genes are expressed and regulated across different cell types. Data prepared by Ricard Argelaguet.

Usage

scMultiome(
  DataType = "pbmc_10x",
  modes = "*",
  version = "1.0.0",
  format = c("MTX", "HDF5"),
  dry.run = TRUE,
  verbose = TRUE,
  ...
)

Arguments

DataType

character(1) Indicates study that produces this type of data (default: 'mouse_gastrulation')

modes

character() A wildcard / glob pattern of modes, such as "acc*". A wildcard of "*" will return all modes including Chromatin Accessibilty ("acc"), Methylation ("met"), RNA-seq ("rna") which is the default.

version

character(1) Either version '1.0.0' or '2.0.0' depending on data version required (default '1.0.0'). See version section.

format

character(1) Either MTX or HDF5 data format (default MTX)

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 10X PBMC MultiAssayExperiment object

Details

Users are able to choose from either an MTX or HDF5 file format as the internal data representation. The MTX (Matrix Market) format allows users to load a sparse dgCMatrix representation. Choosing HDF5 gives users a sparse HDF5Array class object. * pbmc_10x: 10K Peripheral Blood Mononuclear Cells provided by 10x Genomics website Cell quality control filters are available in the object colData together with the celltype annotation labels.

Examples

scMultiome(DataType = "pbmc_10x", modes = "*", dry.run = TRUE)
#>    ah_id    mode file_size           rdataclass rdatadateadded rdatadateremoved
#> 1 EH4624 atac_se    2.6 Mb SingleCellExperiment     2020-09-24             <NA>
#> 2 EH4625    atac  206.5 Mb            dgCMatrix     2020-09-24             <NA>
#> 3 EH6689  rna_se    0.6 Mb SingleCellExperiment     2021-07-16             <NA>
#> 4 EH4629     rna   57.7 Mb            dgCMatrix     2020-09-24             <NA>