CITEseq | R Documentation |
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.
CITEseq(
DataType = c("cord_blood", "peripheral_blood"),
modes = "*",
version = "1.0.0",
dry.run = TRUE,
filtered = FALSE,
verbose = TRUE,
DataClass = c("MultiAssayExperiment", "SingleCellExperiment"),
...
)
DataType |
|
modes |
|
version |
|
dry.run |
|
filtered |
|
verbose |
|
DataClass |
either MultiAssayExperiment or SingleCellExperiment data classes can be returned (default MultiAssayExperiment) |
... |
Additional arguments passed on to the ExperimentHub-class constructor |
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.
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)
.
Dario Righelli
Stoeckius et al. (2017), Mimitou et al. (2019)
mae <- CITEseq(DataType="cord_blood", dry.run=FALSE)
experiments(mae)
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