DSAVEGetTotalVariationPoolSize: DSAVEGetTotalVariationPoolSize

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

Description

Calculates the total variation with a specific pool size.

Usage

DSAVEGetTotalVariationPoolSize(
  data,
  upperBound = 1e+05,
  lowerBound = 0.5,
  poolSizes = NA,
  repetitionPerSize = 30L,
  rescale = TRUE,
  allowSubSampling = FALSE,
  silent = FALSE
)

Arguments

data	a numeric matrix
upperBound	filters out the genes with mean expression higher than this value. Defaults to 100,000, which in practice includes almost all genes.
lowerBound	filters out the genes with mean expression lower than this value. Defaults to 0.5.
poolSizes	list of numeric pool size values, all should be maximum half of the total size of the data in the data object
repetitionPerSize	Positive integer describing how many iterations that are used. Defaults to 30.
rescale	logical, determine if the data should be rescaled. Should normally be TRUE. pool size
allowSubSampling	[optional] If true, the function will reduce the dataset used to 2 times the max pool size used. This is to save memory usage for large datasets. Defaults to FALSE.
silent	(optional) If true, no progress bar is shown. Defaults to FALSE

Details

Calculates the average pairwise total variation between two pools of cells with specific size, with a TPM filtration on the genes.

Value

a list(poolSizes = numeric vector, Rs = numeric vector (R metric for each pool size))

Author(s)

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

Examples

## Not run: DSAVEGetTotalVariationPoolSize(data, poolSize = 50, upperBound = 1000,
lowerBound = 0.01, na.rm = TRUE, seed = 1, repetitionPerSize = 30, 0.5)
## End(Not run)

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