SCUBA

Will generate a trajectory using SCUBA.

This method was wrapped inside a container. The original code of this method is available here.

ti_scuba(rigorous_gap_stats = TRUE, N_dim = 2L,
  low_gene_threshold = 1L, low_gene_fraction_max = 0.7,
  min_split = 15L, min_percentage_split = 0.25)

Arguments

rigorous_gap_stats

Whether to use rigorous gap statistics to determine number of clusters. Default: TRUE. Format: logical.
N_dim

Number of TSNE dimensions. Domain: U(2, 3). Default: 2. Format: integer.
low_gene_threshold

Threshold value for genes of low expression levels. Domain: U(0, 5). Default: 1. Format: numeric.
low_gene_fraction_max

Maximum fraction of lowly-expressed cells allowed for each gene. Domain: U(0, 1). Default: 0.7. Format: numeric.
min_split

Lower threshold on the number of cells in a cluster for this cluster to be split. Domain: U(1, 100). Default: 15. Format: integer.
min_percentage_split

Minimum fraction of cells in the smaller cluster during a bifurcation. Domain: U(0, 1). Default: 0.25. Format: numeric.

Value

A TI method wrapper to be used together with infer_trajectory

References

Marco, E., Karp, R.L., Guo, G., Robson, P., Hart, A.H., Trippa, L., Yuan, G.-C., 2014. Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape. Proceedings of the National Academy of Sciences 111, E5643–E5650.