single.round.QP.analysis: Single Round of Quadratic Programming

In morris-lab/Capybara: A tool to measure cell identity and fate transitions

Single Round of Quadratic Programming

Description

This function runs preprocessing, including log normalization, gene intersection and scaling. Further, run one round of quadratic programming. See function sc.quad.prog.run for detailed description

Usage

single.round.QP.analysis(
  ref,
  sc.data,
  scale.bulk.sc = "scale",
  unix.par = FALSE,
  windows.par = FALSE,
  force.eq = 0,
  n.cores = 1,
  save.to.path,
  save.to.filename,
  bulk.norm = T,
  norm.sc = T,
  log.bulk = T,
  log.sc = T
)

Arguments

ref	The reference transcriptome taht contains the transcriptome of each potential cell type
sc.data	the transcriptome profile of cells from single-cell RNA-sequencing
scale.bulk.sc	either scale or non-scale. Scaling is recommended to make the reference comparable to the single-cell. Default to scale.
unix.par	boolean value, either TRUE or FALSE. If using unix/linux based systems, this command can be set to TRUE to parallelize use parallel package. Default to FALSE
windows.par	boolean value, either TRUE or FALSE. If using Windows based systems, this command can be set to TRUE to parallelize use snow package. Default to FALSE
force.eq	either 0 or 1. Setting to 0 assumes the 1st constraint as inequality. Setting to 1 assumes equality. Default to 0
n.cores	the number of cores to use for parallel processes. If no parallelization selected, no parallelization will be implemented. Only 1 core will be used
save.to.path	which directory would you like to save your file?
save.to.filename	prefix to the filename to save to. The final filename will be constructed inside of the function by tagging the following string _scale.csv for scaling and _non_scale.csv for not scaling.
bulk.norm	boolean value, either TRUE or FALSE. Would you like to normalize the reference?
norm.sc	boolean value, either TRUE or FALSE. Would you like to normalize the single-cell dataset?
log.bulk	boolean value, either TRUE or FALSE. Would you like to log the reference?
log.sc	boolean value, either TRUE or FALSE. Would you like to log the single-cell dataset?

Note

This function calls the quadratic programming referenced to Treutlein et. al.

Examples

single.round.QP.analysis(ref = ref.transcriptome, sc.data = sc.transcriptome, force.eq = 1, save.to.path = "~/Desktop/", save.to.filename = "my_favorite")

morris-lab/Capybara documentation built on June 13, 2022, 10:33 p.m.