runVst: Variance Stabilizing Transformation

In navinlabcode/copykit: CopyKit

Variance Stabilizing Transformation

Description

Performs variance stabilization transformation of the bin counts

Usage

runVst(scCNA, transformation = c("ft", "log"), assay = "bincounts")

Arguments

scCNA	The scCNA object
transformation	A character indicating the variance stabilization transformation to be performed. See runVst details.
assay	A character indicating the assay slot to extract the bincounts for variance stabilization

Details

runVst performs variance stabilization to reduce the overdispersion from the negative binomial distribution nature of the bin counts and reduce technical bias. The argument vst controls the choice of the transformation allowing either the Freeman-Tukey transformation by using the option 'ft' (recommended) or a logarithmic transformation with the option 'log'. Using a 'log' transformation may result in long segmentation times for a few cells with large breakpoint counts.

Value

A slot into the scCNA object containing the variance stabilized matrix.

References

Freeman, M. F.; Tukey, J. W. (1950), "Transformations related to the angular and the square root", The Annals of Mathematical Statistics, 21 (4), pp. 607–611, doi:10.1214/aoms/1177729756, JSTOR 2236611

Examples

copykit_obj <- mock_bincounts(ncells = 10)
copykit_obj <- runVst(copykit_obj)

navinlabcode/copykit documentation built on Sept. 22, 2023, 9:16 a.m.