DSAVEGetGeneVariation: DSAVEGetGeneVariation

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

Description

Calculates the DSAVE gene-wise BTM variation metric.

Usage

DSAVEGetGeneVariation(
  data,
  lb = 10,
  iterations = 100,
  maxNumCells = 2000,
  silent = FALSE
)

Arguments

data	numeric matrix, the input dataset (cell population)
lb	(optional) TPM lower bound, genes below this will not be investigated. Defaults to 10 TPM/CPM.
iterations	(optional) The number of SNO datasets to generate. Recommended value is 100 if no p values are needed, 10,000 - 100,000 if p-values are of interest. Defaults to 100,000.
maxNumCells	(optional) ds is reduced to this number of cells if it contains more, to save computation time. Defaults to 2,000.
silent	(optional) If true, no progress bar is shown. Defaults to FALSE

Value

list(genes, logCVDifference, pVals, SNOVariances, SNOCountsPerGene)

Author(s)

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

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