fit_pseudotime_model: Fit the gene expression profile in pseudotime

In kieranrcampbell/embeddr: Laplacian eigenmaps & principal curves for pseudotemporal ordering of single-cell RNA-seq data

Description

This function fits the expression profile of y as a function of pseudotime using a natural cubic spline of degree three. A tobit model is used to censor values less than min_expr

Usage

fit_pseudotime_model(sce, gene, ...)

Arguments

sce	An object of type SCESet
gene	The gene name to fit, or anything that can subset the SCE model to a single gene
...	Additional arguments to be passed to AER::tobit

Value

An object of class AER::tobit

Examples

library(scater)
data('sc_example_counts') ; sce <- newSCESet(countData = sc_example_counts)
sce <- embeddr(sce)
sce <- fit_pseudotime(sce)
model <- fit_pseudotime_model(sce, 1) # fit for first gene

kieranrcampbell/embeddr documentation built on May 20, 2019, 9:24 a.m.