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

Description Usage Arguments Details Value

View source: R/expr_models.R

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

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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.