newBASiCS_Data {BASiCS} | R Documentation |
Creates a SingleCellExperiment object from a matrix of expression
counts and experimental information about spike-in genes
Description
newBASiCS_Data
creates a
SingleCellExperiment
object from a matrix of expression
counts and experimental information about spike-in genes.
Usage
newBASiCS_Data(
Counts,
Tech = rep(FALSE, nrow(Counts)),
SpikeInfo = NULL,
BatchInfo = NULL,
SpikeType = "ERCC"
)
Arguments
Counts |
Matrix of dimensions q times n whose elements
contain the expression counts to be analyses
(including biological and technical spike-in genes). Gene names must be
stored as rownames(Counts) .
|
Tech |
Logical vector of length q . If Tech = FALSE the
gene is biological; otherwise the gene is spike-in. Defaul value:
Tech = rep(FALSE, nrow(Counts)) .
|
SpikeInfo |
data.frame whose first and second columns contain
the gene names assigned to the spike-in genes (they must match the ones in
rownames(Counts) ) and the associated input number of molecules,
respectively. If SpikeInfo = NULL , only the horizontal integration
implementation (no spikes) can be run. Default value:
SpikeInfo = NULL .
|
BatchInfo |
Vector of length n whose elements indicate batch
information. Not required if a single batch is present on the data.
Default value: BatchInfo = NULL .
|
SpikeType |
Character to indicate what type of spike-ins are in use.
Default value: SpikeType = "ERCC" (parameter is no longer used).
|
Value
An object of class SingleCellExperiment
.
Author(s)
Catalina A. Vallejos cnvallej@uc.cl
Nils Eling eling@ebi.ac.uk
See Also
SingleCellExperiment
[Package
BASiCS version 2.6.0
Index]