transcriptionalVarianceExplained: transcriptionalVarianceExplained

In plger/iPSCpoweR: iPSCpoweR: transcriptomics-based evaluation of experimental designs for iPSC disease modeling

Description

Computes for each gene the variance explained by each variable.

Usage

transcriptionalVarianceExplained(
  res = NULL,
  unit = "tpm",
  logTransform = T,
  variables = c("sex", "individual"),
  doPlot = TRUE,
  mixed = TRUE,
  formula = NULL,
  ncores = NULL
)

Arguments

unit	Either "tpm" (default), "fpkm", or "counts".
logTransform	Logical; whether to log-transform the data (default T).
variables	The explanatory variables to include. Default "sex" and "individual"
doPlot	Logical; whether to plot a summary of the results (default TRUE; requires packages 'beanplot' and 'LSD' to be installed)
mixed	Logical; whether to use mixed models (via 'lme4') (default TRUE).
formula	Specify the formula to use. If specified, this overrides the 'variables' argument. If 'mixed=F', the default formula is '~.'; if 'mixed=T', each variable is considered a random variable.
ncores	The number of threads (by defaults uses all but 1 cores)

Value

a dataframe containing the square residuals, with genes as rows and explanatory variables as columns (plus a first column containing the gene's mean expression).

plger/iPSCpoweR documentation built on Feb. 2, 2022, 1:37 a.m.