BASiCS_VarianceDecomp: Decomposition of gene expression variability according to...
In catavallejos/BASiCS: Bayesian Analysis of Single-Cell Sequencing data

BASiCS_VarianceDecomp

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 = c("BioVarGlobal", "GeneName", "TechVarGlobal", "ShotNoiseGlobal"),
  Plot = TRUE,
  main = "Overall variance decomposition",
  ylab = "% of variance",
  beside = FALSE,
  palette = "Set1",
  legend = c("Biological", "Technical", "Shot noise"),
  names.arg = if (nBatch == 1) "Overall" else c("Overall", paste("Batch",
    seq_len(nBatch)))
)

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`.
`main`	Plot title.
`ylab`	y axis label.
`beside`	If `TRUE`, bars are placed beside each other. If `FALSE`, bars are stacked.
`palette`	Palette to be passed to `scale_fill_brewer` to create a discrete colour mapping.
`legend`	Labels for variance components.
`names.arg`	X axis labels.

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)

catavallejos/BASiCS documentation built on March 27, 2024, 12:49 a.m.