R: Decomposition of gene expression variability according to...

BASiCS_VarianceDecomp {BASiCS}

R Documentation

Decomposition of gene expression variability according to BASiCS

Description

Function to decompose total variability of gene expression into biological and technical components.

Usage

BASiCS_VarianceDecomp(Chain, OrderVariable = "BioVarGlobal", Plot = TRUE,
  ...)

Arguments

`Chain`	an object of class `BASiCS_Chain`
`OrderVariable`	Ordering variable for output. Possible values: `'GeneName'`, `'BioVarGlobal'`, `'TechVarGlobal'` and `'ShotNoiseGlobal'`. Default: `OrderVariable = "BioVarGlobal"`.
`Plot`	If `TRUE`, a barplot of the variance decomposition (global and by batches, if any) is generated. Default: `Plot = TRUE`.
`...`	Other arguments to be passed to `barplot`

Details

See vignette

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 component (overall across all cells)
TechVarGlobal: Percentage of variance explained by the technical component (overall across all cells)
ShotNoiseGlobal: Percentage of variance explained by the shot noise component (baseline Poisson noise, 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.

Author(s)

Catalina A. Vallejos cnvallej@uc.cl

References

Vallejos, Marioni and Richardson (2015). PLoS Computational Biology.

Examples


# For illustration purposes we load a built-in 'BASiCS_Chain' object 
# (obtained using the 'BASiCS_MCMC' function)
data(ChainSC)

VD <- BASiCS_VarianceDecomp(ChainSC)

[Package BASiCS version 1.2.1 Index]