getTraj: Find a plausible developmental journey

In wjawaid/roots: Reconstructing Ordered Ontogenic Trajectories

Description

Return a plausible developmental journey

Usage

getTraj(rdmap, tm, sourceCellInds, terminalCellsInd = NULL, momAdj = 0.5,
  w1 = exp(1), w2 = 1, simLen = 50, sim.seed = NULL, varEst = 10)

Arguments

rdmap	reduced dimensionality matrix with cells in rows and dims in columns
tm	Transition matrix
sourceCellInds	Starting sell indices
terminalCellsInd	Terminal cell indices
momAdj	Weighting to adjust momentum. From 0-1. Lower numbers make smaller adjustment to momentum vector.
w1	Parameter - Base used for modifying of tm probs.
w2	Parameter - Multiplifaction factor used for modifying tm probs.
simLen	Maximum number of allowable tranisitons
sim.seed	Random seed for reproducibility
varEst	Number of alternatives to sample for estimating variance.

Details

Return a plausible developmental journey

Value

Returns a data.frame of ordered indices and momentums

Author(s)

Wajid Jawaid

Examples

## Not run: 
traj <- getTraj(rdmap, tm, startCells, terminalCells)

## End(Not run)

wjawaid/roots documentation built on May 20, 2019, 11:37 a.m.