Get dynamic genes

dynamic_genes(object, ...)

# S4 method for class 'matrix'
dynamic_genes(
  object,
  pseudotime = NULL,
  cores = 1,
  verbose = TRUE,
  adjust_method = "BH",
  ...
)

# S4 method for class 'Seurat'
dynamic_genes(
  object,
  pseudotime_column,
  cores = 1,
  verbose = TRUE,
  adjust_method = "BH",
  layer = "data",
  ...
)

Arguments

object: The input data, a matrix with cells/samples by genes/features or a seurat object.
...: Arguments for other methods
pseudotime: Pseudotime of cells, the length and order should be the same as the expression matrix columns.
cores: The number of cores to use for parallelization with foreach, default is 1.
verbose: Logical value, default is TRUE, whether to print progress messages.
adjust_method: The method used to calculate adjust P-value.
pseudotime_column: The column name in meta_data annotating pseudotime or latent time.
layer: The layer used in Seurat object.

Value

A new object with dynamic genes

Examples

data("example_matrix")
data("example_meta_data")
dynamic_genes(
  object = example_matrix,
  pseudotime = example_meta_data$pseudotime
)
#> ℹ [2025-05-28 02:34:53] Using 1 core
#>    gene       p_value adjust_p_value
#> 2   g10  0.000000e+00   0.000000e+00
#> 3   g11  0.000000e+00   0.000000e+00
#> 4   g12  0.000000e+00   0.000000e+00
#> 5   g13  0.000000e+00   0.000000e+00
#> 6   g14  0.000000e+00   0.000000e+00
#> 7   g15  0.000000e+00   0.000000e+00
#> 8   g16  0.000000e+00   0.000000e+00
#> 9   g17  0.000000e+00   0.000000e+00
#> 10  g18  0.000000e+00   0.000000e+00
#> 13   g4  0.000000e+00   0.000000e+00
#> 14   g5  0.000000e+00   0.000000e+00
#> 15   g6  0.000000e+00   0.000000e+00
#> 16   g7  0.000000e+00   0.000000e+00
#> 17   g8  0.000000e+00   0.000000e+00
#> 18   g9  0.000000e+00   0.000000e+00
#> 12   g3 1.333076e-178  1.499711e-178
#> 1    g1 1.185038e-119  1.254746e-119
#> 11   g2  8.676800e-01   8.676800e-01

if (FALSE) { # \dontrun{
vector_result <- infer_vector(example_matrix)
dynamic_genes(
  object = vector_result$matrix,
  pseudotime = vector_result$pseudotime[, 2]
)
} # }