StatModel               StatModel
StatModel-class         The StatModel class for satuRn
Tasic_counts_vignette   A 'Matrix' with transcript-level counts derived
                        from our case study which builds on the dataset
                        of Tasic et al.  We used Salmon (V1.1.0) to
                        quantify all L5IT cells (both for ALM and VISp
                        tissue) from mice with a normal eye condition.
                        From these cells, we randomly sampled 20 cells
                        of each of the following cell types to use for
                        this vignette; L5_IT_VISp_Hsd11b1_Endou,
                        L5_IT_ALM_Tmem163_Dmrtb1 and L5_IT_ALM_Tnc. The
                        data has already been leniently filtered with
                        the 'filterByExpr' function of edgeR.
Tasic_metadata_vignette
                        Metadata associated with the expression matrix
                        'Tasic_counts_vignette'. See
                        '?Tasic_counts_vignette' for more information
                        on the dataset.
fitDTU                  fitDTU
getModel,StatModel-method
                        Accessor functions for StatModel class
plotDTU                 Plot function to visualize differential
                        transcript usage (DTU)
sumExp_example          A 'SummarizedExperiment' derived from our case
                        study which builds on the dataset of Tasic et
                        al. It contains the same cells as the data
                        object used in the vignette (see
                        '?Tasic_counts_vignette' for more information).
                        In this SummarizedExperiment, we performed a
                        filtering with 'filterByExpr' of edgeR with
                        more stringent than default parameter settings
                        (min.count = 100,min.total.count = 200, large.n
                        = 50, min.prop = 0.9) to reduced the number of
                        retained transcripts. We used this object to
                        create an executable example in the help files
                        of satuRn.
testDTU                 Test function to obtain a top list of
                        transcripts that are differentially used in the
                        contrast of interest
