Inferring a trajectory inference using GPfates

Will generate a trajectory using GPfates.

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

ti_gpfates(log_expression_cutoff = 0.5,
  min_cells_expression_cutoff = 0L, ndim = 2L,
  run_environment = NULL)

Arguments

log_expression_cutoff	numeric; The log expression cutoff (default: 0.5; range: from 0.5 to 5L)
min_cells_expression_cutoff	numeric; The min expression cutoff (default: 0L; range: from 0L to 20L)
ndim	integer; Number of dimensions for dimensionality reduction (default: 2L; range: from 1L to 5L)
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

Lönnberg, T., Svensson, V., James, K.R., Fernandez-Ruiz, D., Sebina, I., Montandon, R., Soon, M.S.F., Fogg, L.G., Nair, A.S., Liligeto, U.N., Stubbington, M.J.T., Ly, L.-H., Bagger, F.O., Zwiessele, M., Lawrence, N.D., Souza-Fonseca-Guimaraes, F., Bunn, P.T., Engwerda, C.R., Heath, W.R., Billker, O., Stegle, O., Haque, A., Teichmann, S.A., 2017. Single-cell RNA-seq and computational analysis using temporal mixture modeling resolves TH1/TFHfate bifurcation in malaria. Science Immunology 2, eaal2192.