genSmoothCurveResiduals {monocle}R Documentation

Fit smooth spline curves and return the residuals matrix

Description

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)

Usage

genSmoothCurveResiduals(cds, trend_formula = "~sm.ns(Pseudotime, df = 3)",
  relative_expr = T, residual_type = "response", cores = 1)

Arguments

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

Value

a data frame containing the data for the fitted spline curves.


[Package monocle version 2.12.0 Index]