Inferring a trajectory inference using TSCAN

Source: R/ti_tscan.R

Will generate a trajectory using TSCAN.

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

ti_tscan(minexpr_percent = 0, minexpr_value = 0, cvcutoff = 0,
  clusternum_lower = 2L, clusternum_upper = 9L, modelNames = "VVV",
  run_environment = NULL)

Arguments

minexpr_percent

numeric; (default: 0; range: from 0 to 1)
minexpr_value

numeric; (default: 0; range: from 0 to 10)
cvcutoff

numeric; (default: 0; range: from 0 to 5)
clusternum_lower

integer; (default: 2L; range: from 2L to 20L)
clusternum_upper

integer; (default: 9L; range: from 2L to 20L)
modelNames

discrete; (default: "VVV"; values: "EII", "VII", "EEI", "VEI", "EVI", "VVI", "EEE", "EVE", "VEE", "VVE", "EEV", "VEV", "EVV", "VVV")
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

Ji, Z., Ji, H., 2016. TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis. Nucleic Acids Research 44, e117–e117.