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 = 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.

### See Also

`BASiCS_Chain`

### 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 1.99.1 Index]