genSmoothCurveResiduals {monocle} | R Documentation |
This function will fit smooth spline curves for the gene expression dynamics along pseudotime in a gene-wise manner and return the corresponding residuals matrix. This function is build on other functions (fit_models and residualsMatrix)
genSmoothCurveResiduals( cds, trend_formula = "~sm.ns(Pseudotime, df = 3)", relative_expr = T, residual_type = "response", cores = 1 )
cds |
a CellDataSet object upon which to perform this operation |
trend_formula |
a formula string specifying the model formula used in fitting the spline curve for each gene/feature. |
relative_expr |
a logic flag to determine whether or not the relative gene expression should be used |
residual_type |
the response desired, as accepted by VGAM's predict function |
cores |
the number of cores to be used while testing each gene for differential expression |
a data frame containing the data for the fitted spline curves.