monocle_fitModel: Fit model function in monocle

In jacobheng/cellwrangler: Supplemental toolkit for single-cell RNAseq analysis

Description

monocle_fitModel() is the fitModel() function found in monocle 2. 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

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

Arguments

cds	a monocle CellDataSet object
modelFormulaStr	model 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.

Value

a vglm object

Examples

monocle_fitModel(dat, modelFormulaStr="~num_genes_expressed+genotype")

jacobheng/cellwrangler documentation built on Aug. 12, 2019, 6:49 a.m.