regressCyclePartial | R Documentation |
Uses a GLM to remove differences between specified cell-cycle phases.
regressCyclePartial(expr_mat, classification, type=c("counts","norm"), method=c("scores", "phase"), phases=c("G2M", "G1S"), allow_negative=FALSE, subsample_cells=ncol(expr_mat))
expr_mat |
a raw or normalized expression matrix to regress |
classification |
output from |
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. |
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.
regressCyclePartial
Uses a glm to regress out differences among a select set of cell cycle phases
classifyCells
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)
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