differentialGeneTest {monocle} | R Documentation |
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.
differentialGeneTest( cds, fullModelFormulaStr = "~sm.ns(Pseudotime, df=3)", reducedModelFormulaStr = "~1", relative_expr = TRUE, cores = 1, verbose = FALSE )
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. |
a data frame containing the p values and q-values from the likelihood ratio tests on the parallel arrays of models.