CITEseq: CITEseq

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

CITEseq

Description

function assembles data on-the-fly from 'ExperimentHub' to provide a MultiAssayExperiment container. Actually the 'dataType' argument provides access to the available datasets associated to the package.

Usage

CITEseq(
  DataType = c("cord_blood", "peripheral_blood"),
  modes = "*",
  version = "1.0.0",
  dry.run = TRUE,
  filtered = FALSE,
  verbose = TRUE,
  DataClass = c("MultiAssayExperiment", "SingleCellExperiment"),
  ...
)

Arguments

DataType	character(1) indicating the identifier of the dataset to retrieve. (default "cord_blood")
modes	character() The assay types or modes of data to obtain these include scADT and scRNA-seq data by default.
version	character(1) Either version '1.0.0' depending on data version required.
dry.run	logical(1) Whether to return the dataset names before actual download (default TRUE)
filtered	logical(1) indicating if the returned dataset needs to have filtered cells. See Details for additional information about the filtering process.
verbose	logical(1) Whether to show the dataset currently being (down)loaded (default TRUE)
DataClass	either MultiAssayExperiment or SingleCellExperiment data classes can be returned (default MultiAssayExperiment)
...	Additional arguments passed on to the ExperimentHub-class constructor

Details

CITEseq data are a combination of single cell transcriptomics and about a hundread of cell surface proteins.

Available datasets are:

• cord_blood: a dataset of single cells of cord blood as provided in Stoeckius et al. (2017).

  • scRNA_Counts - Stoeckius scRNA-seq gene count matrix

  • scADT - Stoeckius antibody-derived tags (ADT) data

• peripheral_blood: a dataset of single cells of peripheral blood as provided in Mimitou et al. (2019). We provide two different conditions controls (CTRL) and Cutaneous T-cell Limphoma (CTCL). Just build appropriate modes regex for subselecting the dataset modes.

  • scRNA - Mimitou scRNA-seq gene count matrix

  • scADT - Mimitou antibody-derived tags (ADT) data

  • scHTO - Mimitou Hashtag Oligo (HTO) data

  • TCRab - Mimitou T-cell Receptors (TCR) alpha and beta available through the object metadata.

  • TCRgd - Mimitou T-cell Receptors (TCR) gamma and delta available through the object metadata.

If 'filtered' parameter is 'FALSE' (default), the 'colData' of the returned object contains multiple columns of 'logicals' indicating the cells to be discarded. In case 'filtered' is 'TRUE', the 'discard' column is used to filer the cells. Column 'adt.discard' indicates the cells to be discarded computed on the ADT assay. Column 'mito.discard' indicates the cells to be discarded computed on the RNA assay and mitocondrial genes. Column 'discard' combines the previous columns with an 'OR' operator. Note that for the 'peripheral_blood' dataset these three columns are computed and returned separately for the 'CTCL' and 'CTRL' conditions. In this case the additional 'discard' column combines the 'discard.CTCL' and 'discard.CTRL' columns with an 'OR' operator. Cell filtering has been computed for 'cord_blood' and 'peripheral_blood' datasets following section 12.3 of the Advanced Single-Cell Analysis with Bioconductor book. Executed code can be retrieved in the CITEseq_filtering.R script of this package.

Value

A single cell multi-modal MultiAssayExperiment or informative 'data.frame' when 'dry.run' is 'TRUE'. When 'DataClass' is 'SingleCellExperiment' an object of this class is returned with an RNA assay as main experiment and other assay(s) as 'AltExp(s)'.

Author(s)

Dario Righelli

References

Stoeckius et al. (2017), Mimitou et al. (2019)

Examples

mae <- CITEseq(DataType="cord_blood", dry.run=FALSE)
experiments(mae)

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