RegressCycle: Regress out cell-cycle

In tallulandrews/CycleMix: Cell-Cycle using Mixture Models

Regress out cell-cycle

Description

Uses a GLM to remove differences between specified cell-cycle phases.

Usage

  regressCyclePartial(expr_mat, classification, type=c("counts","norm"), method=c("scores", "phase"), phases=c("G2M", "G1S"), allow_negative=FALSE, subsample_cells=ncol(expr_mat))

Arguments

expr_mat	a raw or normalized expression matrix to regress
classification	output from classifyCells.
type	whether the expr_mat is raw counts (uses NB-GLM) or normalized expression (uses Gaussian-GLM).
method	which factor to regress on.
phases	which phases to regress out.
allow_negative	whether or not to allow corrected expression values to be negative.

Details

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

regressCyclePartial Uses a glm to regress out differences among a select set of cell cycle phases

See Also

classifyCells

Examples

	require(SingleCellExperiment)
	classification <- classifyCells(Ex,  MGeneSets$Cyclone, do.scale=TRUE, allow.multi=FALSE);
	Ex <- regressCyclePartial(counts(Ex), classification, type="counts", method="scores", phases=c("G1", "S", "G2M"), allow_negative=TRUE, subsample_cells=200)
	Ex <- regressCyclePartial(counts(Ex), classification, type="counts", method="phase", phases=c("G1", "S", "G2M"), allow_negative=TRUE, subsample_cells=200)
	regressed_mat1 <- regressCyclePartial(logcounts(Ex), classification, type="norm", method="scores", phases=c("G1", "S", "G2M"), allow_negative=FALSE, subsample_cells=200)
	regressed_mat2 <- regressCyclePartial(logcounts(Ex), classification, type="norm", method="phase", phases=c("G1", "S", "G2M"), allow_negative=TRUE, subsample_cells=200)

tallulandrews/CycleMix documentation built on July 3, 2025, 11:41 p.m.