fitModel: Fits a model for each gene in a CellDataSet object.

In cole-trapnell-lab/monocle-release: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

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

cole-trapnell-lab/monocle-release documentation built on May 13, 2019, 8:50 p.m.