scde.expression.magnitude: Return scaled expression magnitude estimates

In hms-dbmi/scde: Single Cell Differential Expression

Return scaled expression magnitude estimates

Description

Return point estimates of expression magnitudes of each gene across a set of cells, based on the regression slopes determined during the model fitting procedure.

Usage

scde.expression.magnitude(models, counts)

Arguments

models	models determined by scde.error.models
counts	count matrix

Value

a matrix of expression magnitudes on a log scale (rows - genes, columns - cells)

Examples

data(es.mef.small)
cd <- clean.counts(es.mef.small, min.lib.size=1000, min.reads = 1, min.detected = 1)
data(o.ifm)  # Load precomputed model. Use ?scde.error.models to see how o.ifm was generated
# get expression magnitude estimates
lfpm <- scde.expression.magnitude(o.ifm, cd)

hms-dbmi/scde documentation built on April 19, 2023, 10:21 p.m.