genSmoothCurves {monocle} | R Documentation

## Fit smooth spline curves and return the response 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 response matrix. This function is build on other functions (fit_models and responseMatrix) and used in calILRs and calABCs functions

### Usage

    genSmoothCurves(cds, new_data, trend_formula = "~sm.ns(Pseudotime, df = 3)",
      relative_expr = T, response_type = "response", cores = 1)

### Arguments

`cds` | a CellDataSet object upon which to perform this operation
`new_data` | a data.frame object including columns (for example, Pseudotime) with names specified in the model formula. The values in the data.frame should be consist with the corresponding values from cds object.
`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
`response_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 2.15.0 Index]