sc.quad.prog.run: Single-Cell Quadratic Programming Calculation

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

Single-Cell Quadratic Programming Calculation

Description

This function runs quadratic programming to identify the probability of the cells in single-cell RNA-seq belonging to cell types in the reference transcriptome

Usage

sc.quad.prog.run(
  bulk.transcriptome,
  single.cell.transcriptome,
  force.eq = 0,
  unix.parallel = FALSE,
  windows.parallel = FALSE,
  parallel.cores = 4
)

Arguments

bulk.transcriptome	The reference transcriptome taht contains the transcriptome of each potential cell type
single.cell.transcriptome	the transcriptome profile of cells from single-cell RNA-sequencing
force.eq	either 0 or 1. Setting to 0 assumes the 1st constraint as inequality. Setting to 1 assumes equality. Default to 0
unix.parallel	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.parallel	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
parallel.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

Note

Code reference from Treutlein et. al., Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq

Examples

sc.quad.prog.run(ref.transcriptome, sc.transcriptome, force.eq = 1)

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