Model fit and checkContain the fitGam function used to fit the model, as well as functions to check the fit, extract components and decide on the appropriate number of knots. 


fitGAM 

Evaluate the optimal number of knots required for fitGAM. 

knots 

Get smoother pvalue as returned by 

Get smoother Chisquared test statistics. 

TestsAll tests currently implemented in tradeSeq. All tests are of the form xxxTest. Tests can either be run in an omnibus fashion (all lineages) or on an individual basis (lineages for withinlineage tests, and pairwise form betweenlineages tests). 

Perform statistical test to check whether gene expression is constant across pseudotime within a lineage 

Perform statistical test to check for DE between final stages of every lineage. 

Perform test of early differences between lineages 

Assess differential expression pattern between lineages. 

Perform statistical test to check for DE between starting point and the end stages of every lineage 

VisualizationFunctions to plot the results 

Plot gene expression in reduced dimension. 

Plot the logtransformed counts and the fitted values for a particular gene along all lineages 

DataThe dataset used in example 

A list of GAM models, used to demonstrate the various tests. 

A vector defining cell types, used in the package vignette. 

A count matrix, used in the package vignette. 

A SlingshotDataset object, used in the package vignette. 

A SlingshotDataset object, used in the package unit tests. 

ClusteringClustering of gene expression patterns 


Cluster gene expression patterns. 
predictCells 

predictSmooth 