BASiCS (version 0.3.1)

BASiCS_VarianceDecomp: Decomposition of gene expression variability according to BASiCS

Description

Decomposition of gene expression variability according to BASiCS

Usage

BASiCS_VarianceDecomp(Data, object, OrderVariable = "BioVarGlobal",
  Plot = TRUE, ...)

Arguments

Data

an object of class BASiCS_Data-class

object

an object of class BASiCS_Chain-class

OrderVariable

Ordering variable for output. Must take values in c("GeneNames", "BioVarGlobal", "TechVarGlobal", "ShotNoiseGlobal").

Plot

If TRUE, a barplot of the variance decomposition (global and by batches, if any) is generated

...

Other arguments to be passed to barplot

GeneNames

Vector of characters containing gene names (must be in the same order as in the Counts matrix).

Value

A data.frame whose first 4 columns correspond to

GeneName

Gene name (as indicated by user)

BioVarGlobal

Percentage of variance explained by a biological cell-to-cell heterogeneity component (overall across all cells)

TechVarGlobal

Percentage of variance explained by the technical cell-to-cell heterogeneity component (overall across all cells)

ShotNoiseGlobal

Percentage of variance explained by the shot noise component (baseline, overall across all cells)

If more than 1 batch of cells are being analysed, the remaining columns contain the corresponding variance decomposition calculated within each batch.

Details

See vignette

References

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

See Also

BASiCS_Chain-class

Examples

# NOT RUN {
# See
help(BASiCS_MCMC)
# }