newBASiCS_Data {BASiCS} | R Documentation |
newBASiCS_Data
creates a
SingleCellExperiment
object from a matrix of expression
counts and experimental information about spike-in genes.
newBASiCS_Data(Counts, Tech = rep(FALSE, nrow(Counts)), SpikeInfo = NULL, BatchInfo = NULL, SpikeType = "ERCC")
Counts |
Matrix of dimensions |
Tech |
Logical vector of length |
SpikeInfo |
|
BatchInfo |
Vector of length |
SpikeType |
Character to indicate what type of spike-ins are in use.
For more details see argument 'type' in
see 'help(isSpike, package = "SingleCellExperiment")'. Default value:
|
An object of class SingleCellExperiment
.
Catalina A. Vallejos cnvallej@uc.cl
Nils Eling eling@ebi.ac.uk
## Data with spike-ins # Expression counts set.seed(1) Counts <- matrix(rpois(50*10, 2), ncol = 10) rownames(Counts) <- c(paste0('Gene', 1:40), paste0('ERCC', 1:10)) # Technical information Tech <- grepl("ERCC", rownames(Counts)) # Spikes input number of molecules set.seed(2) SpikeInfo <- data.frame(gene = rownames(Counts)[Tech], amount = rgamma(10, 1, 1)) # Creating a BASiCS_Data object (no batch effect) DataExample <- newBASiCS_Data(Counts, Tech = Tech, SpikeInfo = SpikeInfo) # Creating a BASiCS_Data object (with batch effect) BatchInfo <- c(rep(1, 5), rep(2, 5)) DataExample <- newBASiCS_Data(Counts, Tech = Tech, SpikeInfo = SpikeInfo, BatchInfo = BatchInfo) ## Data without spike-ins (BatchInfo is required) # Expression counts set.seed(1) Counts <- matrix(rpois(50*10, 2), ncol = 10) rownames(Counts) <- paste0('Gene', 1:50) BatchInfo <- c(rep(1, 5), rep(2, 5)) # Creating a BASiCS_Data object (with batch effect) DataExample <- newBASiCS_Data(Counts, BatchInfo = BatchInfo)