Inferring a trajectory inference using cellTree with vem

Will generate a trajectory using cellTree with vem.

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

ti_celltree_vem(method = "VEM", sd_filter = 0.5, absolute_width = 0,
  width_scale_factor = 1.5, outlier_tolerance_factor = 0.1,
  rooting_method = "null", num_topics = 4, tot_iter = 1e+06,
  tolerance = 1e-05, run_environment = NULL)

Arguments

method	discrete; (default: "VEM"; values: "VEM")
sd_filter	numeric; (default: 0.5; range: from 0.01 to 5)
absolute_width	numeric; (default: 0; range: from NULL to NULL)
width_scale_factor	numeric; (default: 1.5; range: from 0.1 to 100)
outlier_tolerance_factor	numeric; (default: 0.1; range: from 1e-04 to 1000)
rooting_method	discrete; (default: "null"; values: "longest.path", "center.start.group", "average.start.group", "null")
num_topics	integer; (default: 4; range: from 2 to 15)
tot_iter	numeric; (default: 1e+06; range: from 10000 to 1e+07)
tolerance	numeric; (default: 1e-05; range: from 1e-07 to 0.001)
run_environment	In which environment to run the method, can be "docker" or "singularity".

Value

A TI method wrapper to be used together with infer_trajectory

References

duVerle, D.A., Yotsukura, S., Nomura, S., Aburatani, H., Tsuda, K., 2016. CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data. BMC Bioinformatics 17.