Trajectory inference with TInGa
traj_tinga.RdThis function is a wrapper aroung dynverse functions and TInGa
Usage
traj_tinga(
sobj = NULL,
expression_assay = "RNA",
expression_slot = "data",
count_assay = "RNA",
count_slot = "counts",
dimred_name = "pca",
dimred_max_dim = NULL,
seed = 1337L,
root_cell_id = NULL,
tinga_parameters = list(max_iter = 10000, max_nodes = 10, epsilon_b = 0.05, epsilon_n =
0.001, age_max = 200, lambda = 200, alpha = 0.5, beta = 0.99),
verbose = TRUE
)Arguments
- sobj
A Seurat object (no default)
- expression_assay
CHARACTER : in which assay is the normalized expression ? (default to 'RNA')
- expression_slot
CHARACTER : in which slot from the expression_assay is the normalized expression ? (default to 'data')
- count_assay
CHARACTER : in which assay are the raw counts ? (default to 'RNA')
- count_slot
CHARACTER : in which slot from the count_assay are the raw counts ? (default to 'counts')
- dimred_name
CHARACTER : which reduction to use as a TInGa prior ? (default to 'pca')
- dimred_max_dim
CHARACTER : how many dimensions to use from the reduction (default to NULL, i.e. all dimensions)
- seed
INTEGER : a seed to run TInGa (default to 1337L)
- root_cell_id
CHARACTER : who is the root cell ? (no default)
- tinga_parameters
LIST : a named list with TInGa parameters. Here are all possible values and default (min tested - max tested) : max_iter : 10000 (10000) max_nodes : 10 (4 - 30) epsilon_b : 0.05 (0.005 - 1) epsilon_n : 0.001 (0.0001 - 1) age_max : 200 (100 - 500) lambda : 200 (100 - 500) alpha : 0.5, (0.1 - 0.9) beta : 0.99 Only max_nodes is not set to the default value of TInGa (default to 30 in TInGa).
- verbose
LOGICAL : whether to print verbose or not (default to TRUE)