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 2.21.1 Index]