Inferring a trajectory inference using cellTree with maptpx

Will generate a trajectory using cellTree with maptpx.

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

ti_celltree_maptpx(method = "maptpx", sd_filter = 0.5,
  absolute_width = 0, width_scale_factor = 1.5,
  outlier_tolerance_factor = 0.1, rooting_method = "null",
  num_topics_lower = 2, num_topics_upper = 15, tot_iter = 1e+06,
  tolerance = 0.05, run_environment = NULL)

Arguments

method	discrete; (default: "maptpx"; values: "maptpx")
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_lower	integer; (default: 2; range: from 2 to 15)
num_topics_upper	integer; (default: 15; range: from 2 to 15)
tot_iter	numeric; (default: 1e+06; range: from 10000 to 1e+07)
tolerance	numeric; (default: 0.05; range: from 0.001 to 0.5)
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.