BASiCS (version 1.1.0)

BASiCS_DetectHVG: 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).

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 \(\mu_i\)

Delta

Vector of length q.bio. For each biological gene, posterior median of gene-specific biological over-dispersion parameter \(\delta_i\)

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.

Details

See vignette

References

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

See Also

'>BASiCS_Chain

Examples

# NOT RUN {
# See
help(BASiCS_MCMC)

# }