DSAVECalcBTMScore: DSAVECalcBTMScore

In SysBioChalmers/DSAVE-R: DSAVE: Tools to Investigate Variation and Purity of Subpopulations in Single-Cell RNA-Seq Data

Description

Calculates the DSAVE BTM Variation Score, which gives and overall score for the BTM variation across all genes. This metric is comparable across datasets.

Usage

DSAVECalcBTMScore(
  data,
  templInfo,
  skipAlignment = FALSE,
  iterations = 15,
  useLogTransform = FALSE,
  logTPMAddon = 1,
  silent = FALSE
)

Arguments

data	numeric matrix (can be sparse), the input dataset (cell population)
templInfo	template information
skipAlignment	logical, default FALSE. If FALSE, alignment will be done against the template data
iterations	number of iterations; defaults to 15
useLogTransform	default FALSE, if TRUE calculation will be done on log transformed data
logTPMAddon	default 1, when using log transformed data, this number is added to the data before transforming to avoid log(0)
silent	(optional) If true, no progress bar is shown. Defaults to FALSE

Details

The function generates sampling noise only (SNO) datasets for comparison with the real data, and subtracts the SNO total variation (which is sampling noise only) from the total variation of the cell population, yielding the BTM variation. Cell population alignment makes the metric comparable across cell populations and datasets.

Value

List containing total variation from the aligned and SNO cell populations over the gene expression range, the difference between those, the corresponding gene expression values, and finally the BTM score.

Author(s)

Juan Inda, <[e-mail]>, Johan Gustafsson, <[e-mail]>

Examples

## Not run:  a = DSAVECalcBTMScore(data, templInfo)

SysBioChalmers/DSAVE-R documentation built on Oct. 19, 2021, 11:37 p.m.