pseudotime: Generic to extract pseudotime from CDS object

In cole-trapnell-lab/monocle3: Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

Generic to extract pseudotime from CDS object

Description

Generic to extract pseudotime from CDS object

Usage

pseudotime(x, reduction_method = "UMAP")

Arguments

x	A cell_data_set object.
reduction_method	Reduced dimension to extract pseudotime for.

Value

Pseudotime values.

Examples

 
   cell_metadata <- readRDS(system.file('extdata',
                            'worm_embryo/worm_embryo_coldata.rds',
                            package='monocle3'))
   gene_metadata <- readRDS(system.file('extdata',
                                        'worm_embryo/worm_embryo_rowdata.rds',
                                        package='monocle3'))
   expression_matrix <- readRDS(system.file('extdata',
                                            'worm_embryo/worm_embryo_expression_matrix.rds',
                                             package='monocle3'))

   cds <- new_cell_data_set(expression_data=expression_matrix,
                            cell_metadata=cell_metadata,
                            gene_metadata=gene_metadata)

   cds <- preprocess_cds(cds, num_dim=50)
   cds <- align_cds(cds, alignment_group = "batch",
                    residual_model_formula_str = "~ bg.300.loading + bg.400.loading +
                    bg.500.1.loading + bg.500.2.loading + bg.r17.loading + bg.b01.loading +
                    bg.b02.loading")
   cds <- reduce_dimension(cds) 
   ciliated_genes <- c("che-1", "hlh-17", "nhr-6", "dmd-6", "ceh-36", "ham-1")
   cds <- cluster_cells(cds)
   cds <- learn_graph(cds)
   cds <- order_cells(cds,root_pr_nodes='Y_27')
   ps_tim <- pseudotime(cds)
 

cole-trapnell-lab/monocle3 documentation built on April 7, 2024, 9:24 p.m.