differentialGeneTest: Test genes for differential expression

In monocle: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Description

Tests each gene for differential expression as a function of pseudotime or according to other covariates as specified. differentialGeneTest is Monocle's main differential analysis routine. It accepts a CellDataSet and two model formulae as input, which specify generalized lineage models as implemented by the VGAM package.

Usage

differentialGeneTest(cds, fullModelFormulaStr = "~sm.ns(Pseudotime, df=3)",
  reducedModelFormulaStr = "~1", relative_expr = TRUE, cores = 1,
  verbose = FALSE)

Arguments

cds	a CellDataSet object upon which to perform this operation
fullModelFormulaStr	a formula string specifying the full model in differential expression tests (i.e. likelihood ratio tests) for each gene/feature.
reducedModelFormulaStr	a formula string specifying the reduced model in differential expression tests (i.e. likelihood ratio tests) for each gene/feature.
relative_expr	Whether to transform expression into relative values.
cores	the number of cores to be used while testing each gene for differential expression.
verbose	Whether to show VGAM errors and warnings. Only valid for cores = 1.

Value

a data frame containing the p values and q-values from the likelihood ratio tests on the parallel arrays of models.

See Also

vglm

monocle documentation built on Nov. 8, 2020, 5:06 p.m.