scde.test.gene.expression.difference: Test differential expression and plot posteriors for a...

In hms-dbmi/scde: Single Cell Differential Expression

Test differential expression and plot posteriors for a particular gene

Description

The function performs differential expression test and optionally plots posteriors for a specified gene.

Usage

scde.test.gene.expression.difference(gene, models, counts, prior,
  groups = NULL, batch = NULL, batch.models = models,
  n.randomizations = 1000, show.plots = TRUE, return.details = FALSE,
  verbose = FALSE, ratio.range = NULL, show.individual.posteriors = TRUE,
  n.cores = 1)

Arguments

gene	name of the gene to be tested
models	models
counts	read count matrix (must contain the row corresponding to the specified gene)
prior	expression magnitude prior
groups	a two-level factor specifying between which cells (rows of the models matrix) the comparison should be made
batch	optional multi-level factor assigning the cells (rows of the model matrix) to different batches that should be controlled for (e.g. two or more biological replicates). The expression difference estimate will then take into account the likely difference between the two groups that is explained solely by their difference in batch composition. Not all batch configuration may be corrected this way.
batch.models	optional set of models for batch comparison (typically the same as models, but can be more extensive, or recalculated within each batch)
n.randomizations	number of bootstrap/sampling iterations that should be performed
show.plots	whether the plots should be shown
return.details	whether the posterior should be returned
verbose	set to T for some status output
ratio.range	optionally specifies the range of the log2 expression ratio plot
show.individual.posteriors	whether the individual cell expression posteriors should be plotted
n.cores	number of cores to use (default = 1)

Value

by default returns MLE of log2 expression difference, 95

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
o.prior <- scde.expression.prior(models = o.ifm, counts = cd, length.out = 400, show.plot = FALSE)
scde.test.gene.expression.difference("Tdh", models = o.ifm, counts = cd, prior = o.prior)

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