RegressCycle: Regress out cell-cycle

In tallulandrews/CycleMix: Cell-Cycle using Mixture Models

Regress out cell-cycle

Description

A wrapper for scater's normalizeExprs function to regress out the cell-cycle from a dataset. Or for glm to regress out differences between specific cell-cycle phases.

Usage

  regressCycle_partial(SCE, classification, expr_name="logcounts", method=c("scores", "phase"), phases=c("G2M", "G1S"))
  regressCycle_scater(SCE, classification, expr_name="logcounts", method=c("scores", "phase"))

Arguments

SCE	a SingleCellExperiment object.
classification	output from classifyCells.
expr_name	name of the expression matrix to use, must be an element of assays(SCE).
method	which factor to regress on.
phases	which phases to regress out.

Details

regressCycle_scater Creates a design matrix based on either the phase-signatures ("scores") or the phase assignments ("phase"). Then runs normalizeExprs from the scater package to regress out the cell-cycle.

regressCycle_partial Creates a design matrix based on either the phase-signatures ("scores") or the phase assignments ("phase"). Uses a GLM to remove differences between the provided set of phases.

Value

regressCycle_scater The input SingleCellExperiment object with the regressed expression saved to the 'norm_exprs' slot. regressCycle_partial Uses a glm to regress out differences among a select set of cell cycle phases

See Also

normalizeExprs, classifyCells

Examples

	classification <- classifyCells(Ex,  MGeneSets$Cyclone, do.scale=TRUE, allow.multi=FALSE);
	Ex <- regressCycle_partial(Ex, classification, method="scores", phases=c("G1", "S", "G2M"))
	Ex <- regressCycle_partial(Ex, classification, method="phase", phases=c("G1", "S", "G2M"))
	Ex <- regressCycle_scater(Ex, classification, method="phase")

tallulandrews/CycleMix documentation built on Sept. 28, 2022, 6:55 p.m.