fitModel {monocle} | R Documentation

## Fits a model for each gene in a CellDataSet object.

### Description

This function fits a vector generalized additive model (VGAM) from the VGAM package for each gene in a CellDataSet. By default, expression levels are modeled as smooth functions of the Pseudotime value of each cell. That is, expression is a function of progress through the biological process. More complicated formulae can be provided to account for additional covariates (e.g. day collected, genotype of cells, media conditions, etc).

### Usage

    fitModel(cds, modelFormulaStr = "~sm.ns(Pseudotime, df=3)",
      relative_expr = TRUE, cores = 1)

### Arguments

`cds` | the CellDataSet upon which to perform this operation
`modelFormulaStr` | a formula string specifying the model to fit for the genes.
`relative_expr` | Whether to fit a model to relative or absolute expression. Only meaningful for count-based expression data. If TRUE, counts are normalized by Size_Factor prior to fitting.
`cores` | the number of processor cores to be used during fitting.

### Details

This function fits a vector generalized additive model (VGAM) from the VGAM package for each gene in a CellDataSet. By default, expression levels are modeled as smooth functions of the Pseudotime value of each cell. That is, expression is a function of progress through the biological process. More complicated formulae can be provided to account for additional covariates (e.g. day collected, genotype of cells, media conditions, etc).

### Value

a list of VGAM model objects

[Package monocle version 2.12.0 Index]