CellTrails

Will generate a trajectory using CellTrails.

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

ti_celltrails(filter_features = FALSE, threshold_dl = 2L,
  threshold_cov = 0.05, threshold_ff = 1.7, min_expr = 0L,
  frac = 100L, min_size = 0.01, min_feat = 5L, max_pval = 1e-04,
  min_fc = 2L, l = 10L)

Arguments

filter_features

Whether to include celltrails feature filtering. Default: FALSE. Format: logical.
threshold_dl

Minimum number of samples; if value < 1 it is interpreted as fraction, otherwise as absolute sample count. Domain: U(0, 100). Default: 2. Format: integer.
threshold_cov

Minimum coefficient of variation; numeric value between 0 and 1. Domain: U(0, 1). Default: 0.05. Format: numeric.
threshold_ff

A Z-score cutoff. Domain: U(0, 5). Default: 1.7. Format: numeric.
min_expr

Minimum average feature expression. Domain: U(0, 2). Default: 0. Format: numeric.
frac

Fraction or number (if frac > 1) of eigengaps used to perform linear fit. Domain: e^U(0.00, 6.91). Default: 100. Format: numeric.
min_size

The initial cluster dedrogram is cut at an height such that the minimum cluster size is at least min_size; if min_size < 1 than the fraction of total samples is used, otherwise it is used as absoulte count. Domain: e^U(-6.91, 0.00). Default: 0.01. Format: numeric.
min_feat

Minimum number of differentially expressed features between siblings. If this number is not reached, two neighboring clusters (siblings) in the pruned dendrogram get joined. Domain: U(1, 100). Default: 5. Format: integer.
max_pval

Maximum P-value for differential expression computation. Domain: e^U(-16.12, 0.00). Default: 1e-04. Format: numeric.
min_fc

Mimimum fold-change for differential expression computation. Domain: U(0, 5). Default: 2. Format: numeric.
l

Neighborhood size. Domain: U(1, 50). Default: 10. Format: integer.

Value

A TI method wrapper to be used together with infer_trajectory

References

Ellwanger, D.C., Scheibinger, M., Dumont, R.A., Barr-Gillespie, P.G., Heller, S., 2018. Transcriptional Dynamics of Hair-Bundle Morphogenesis Revealed with CellTrails. Cell Reports 23, 2901–2914.e14.