DSAVEGetTotalVariationFromBulk: DSAVEGetTotalVariationFromBulk

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

Description

Calculate total variation from bulk sample

Usage

DSAVEGetTotalVariationFromBulk(
  data,
  pool4samples,
  upperBound = 1e+05,
  lowerBound = 0.5,
  na.rm = TRUE,
  nComb = 1000L,
  rescale = TRUE
)

Arguments

data	a numericl matrix
pool4samples	logic value, if TRUE, the function will compare the mean of 4 randomly selected samples with the mean of 4 others
upperBound	filters out the genes with mean expression higher than this value
lowerBound	filters out the genes with mean expression lower than this value
na.rm	logical, sends na.rm value to the rowMeans function
nComb	number of combinations
rescale	logical, determine if the data should be rescaled to TPM

Details

Calculates the average pairwise total variation between a list of bulk samples, with a TPM filtration on the genes. If pool4samples is true, it will compare the mean of 4 randomly selected samples with the mean of 4 others. This expects a list of 8 samples.

Value

numeric vector

Author(s)

Juan Inda, <[e-mail]>

Examples

## Not run: DSAVEGetTotalVariationFromBulk(sample, pool4samples = FALSE, upperBound = 100000,
lowerBound = 0.5)
## End(Not run)

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