BASiCS_DetectHVG {BASiCS} | R Documentation

## Detection method for highly and lowly variable genes

### Description

Functions to detect highly and lowly variable genes

### Usage

    BASiCS_DetectHVG(Chain, VarThreshold, ProbThreshold = NULL, EFDR = 0.1,
      OrderVariable = "Prob", Plot = FALSE, ...)

    BASiCS_DetectLVG(Chain, VarThreshold, ProbThreshold = NULL, EFDR = 0.1,
      OrderVariable = "Prob", Plot = FALSE, ...)

### Arguments

`Chain` | an object of class `BASiCS_Chain`
`VarThreshold` | Variance contribution threshold (must be a positive value, between 0 and 1)
`ProbThreshold` | Optional parameter. Posterior probability threshold (must be a positive value, between 0 and 1)
`EFDR` | Target for expected false discovery rate related to HVG/LVG detection (default = 0.10)
`OrderVariable` | Ordering variable for output. Possible values: `'GeneIndex'`, `'Mu'`, `'Delta'`, `'Sigma'` and `'Prob'`.
`Plot` | If `Plot = TRUE` error control and expression versus HVG/LVG probability plots are generated
`...` | Graphical parameters (see `par`).

### Details

See vignette

### Value

`BASiCS_DetectHVG` returns a list of 4 elements:

`Table`

  Matrix whose columns contain

`GeneIndex`

  Vector of length `q.bio`. Gene index as in the order present in the analysed `SingleCellExperiment`

`GeneName`

  Vector of length `q.bio`. Gene name as in the order present in the analysed `SingleCellExperiment`

`Mu`

  Vector of length `q.bio`. For each biological gene, posterior median of gene-specific mean expression parameters μ_i

`Delta`

  Vector of length `q.bio`. For each biological gene, posterior median of gene-specific biological over-dispersion parameter δ_i

`Sigma`

  Vector of length `q.bio`. For each biological gene, proportion of the total variability that is due to a biological heterogeneity component.

`Prob`

  Vector of length `q.bio`. For each biological gene, probability of being highly variable according to the given thresholds.

`HVG`

  Vector of length `q.bio`. For each biological gene, indicator of being detected as highly variable according to the given thresholds.

`ProbThreshold`

  Posterior probability threshold.

`EFDR`

  Expected false discovery rate for the given thresholds.

`EFNR`

  Expected false negative rate for the given thresholds.

`BASiCS_DetectLVG` produces a similar output, replacing the column `HVG` by `LVG`, an indicator of a gene being detected as lowly variable according to the given thresholds.

### Author(s)

Catalina A. Vallejos cnvallej@uc.cl

### References

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

### See Also

`BASiCS_Chain`

### Examples

    # See
    help(BASiCS_MCMC)

[Package BASiCS version 1.4.7 Index]