Trajectory inference
traj_inference.RdThis function is a wrapper around dynverse functions
Usage
traj_inference(
sobj,
ti_method,
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,
verbose = TRUE
)Arguments
- sobj
A Seurat object (no default)
- ti_method
dynmethods : trajectory inference function, from dynmethods package, for instance, dynmethods::ti_slingshot (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 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 infer trajectory (default to 1337L)
- root_cell_id
CHARACTER : who is the root cell ? (no default)
- verbose
LOGICAL : whether to print verbose or not (default to TRUE)