Will generate a trajectory using reCAT.
This method was wrapped inside a container. The original code of this method is available here.
ti_recat(TSPFold = 2, beginNum = 10, endNum = 15, step_size = 2, base_cycle_range_start = 6, base_cycle_range_end = 9, max_num = 300, clustMethod = "GMM", run_environment = NULL)
| TSPFold | integer; No documentation provided by authors (default: |
|---|---|
| beginNum | integer; No documentation provided by authors (default: |
| endNum | integer; No documentation provided by authors (default: |
| step_size | integer; Determines the number of k to skip in your consensus
path, ie ifstep_size = 2, then reCAT would only calculate and merge the paths
fork = 12, 14, 16, 18, ..., n-2, n. We recommend step_size of up to a maximum
of 5 while preserving the performance of reCAT. Usually a step_size of 2 (by
default) would suffice and bigger steps are recommended for larger datasets
(>1000 cells) in order to reduce computational time. (default: |
| base_cycle_range_start | integer; The minimal number of four k's for
computing the reference cycle mentioned in the manuscript. Can be set to 6 or 7
(default: |
| base_cycle_range_end | integer; The maximal number of four k's for
computing the reference cycle mentioned in the manuscript. Can be set to 6 or 7
(default: |
| max_num | integer; No documentation provided by authors (default: |
| clustMethod | discrete; No documentation provided by authors (default:
|
| run_environment | In which environment to run the method, can be |
A TI method wrapper to be used together with
infer_trajectory
Liu, Z., Lou, H., Xie, K., Wang, H., Chen, N., Aparicio, O.M., Zhang, M.Q., Jiang, R., Chen, T., 2017. Reconstructing cell cycle pseudo time-series via single-cell transcriptome data. Nature Communications 8.