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

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

regressCycleScater 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.

regressCyclePartial 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

regressCycleScater The input SingleCellExperiment object with the regressed expression saved to the 'norm_exprs' slot. regressCyclePartial 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 <- regressCyclePartial(Ex, classification, method="scores", phases=c("G1", "S", "G2M"))
	Ex <- regressCyclePartial(Ex, classification, method="phase", phases=c("G1", "S", "G2M"))
	Ex <- regressCycleScater(Ex, classification, method="phase")

tallulandrews/CycleMix documentation built on Dec. 7, 2024, 1:06 p.m.