BASiCS (version 0.3.1)

BASiCS_Data-class: The BASiCS_Data class

Description

Container of expression counts from single-cell sequencing experiments in the format required by BASiCS (see Vallejos et al 2015).

Slots

Counts

Matrix of dimensions q times n whose elements corresponds to the raw expression counts. First q.bio rows correspond to biological genes. Last q-q.bio rows correspond to technical spike-in genes.

Tech

Logical vector of length q. If Tech = F the gene is biological; otherwise the gene is spike-in.

SpikeInput

Vector of length q-q.bio whose elements indicate the input number of molecules for the spike-in genes (amount per cell).

GeneNames

Vector of length q containing gene names. Default value: GeneNames = paste("Gene", 1:q), with numbering order as in the input dataset.

BatchInfo

Vector of lenght n containing batch indicators.

References

Vallejos, Marioni and Richardson (2015). Bayesian Analysis of Single-Cell Sequencing data.

See Also

BASiCS_Data-methods, BASiCS_MCMC.

Examples

# NOT RUN {
Counts = matrix(rpois(10*5, 1), ncol = 5)
Tech = c(rep(FALSE,7),rep(TRUE,3))
SpikeInput = rgamma(3,1,1)
Data = newBASiCS_Data(Counts, Tech, SpikeInput)

head(counts(Data))
dim(counts(Data, type="biological"))
dim(counts(Data, type="technical"))
displayTechIndicator(Data)
displaySpikeInput(Data)
displayBatchInfo(Data)
# }