testPathForDirectionality: Test a path for directionality

In AnnaLaddach/TrajectoryGeometry: This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns

Test a path for directionality

Description

This is the core function of this package. It takes a path, and a choice of statistical measure and computes a statistical significance for the directionality of that path.

Usage

testPathForDirectionality(
  path,
  from = 1,
  to = nrow(path),
  d = ncol(path),
  randomizationParams,
  statistic,
  N
)

Arguments

path	- An n x m matrix representing a series of n points in dimension m.
from	- The starting place along the path which will be treated as the center of the sphere. This defaults to 1.
to	- The end point of the path. This defaults to nrow(path).
d	- The dimension under consideration. This defaults to ncol(path)
randomizationParams	- A character vector which is used to control the production of randomized paths for comparison.
statistic	- Allowable values are 'median', 'mean' or 'max'
N	- The number of random paths to generated for statistical comparison to the given path.

Value

This returns a list giving whose entries are: pValue - the p-value for the path and statistic in question; sphericalData - a list containing the projections of the path to the sphere, the center of that sphere and the statistic for distance to that center; randomDistances - the corresponding distances for randomly chosen; paths; randomizationParams - the choice of randomization parameters

Examples

randomizationParams = c('byPermutation','permuteWithinColumns')
p = testPathForDirectionality(path=straight_path,
                              randomizationParams=randomizationParams,
                              statistic='median',N=100)
q = testPathForDirectionality(path=crooked_path,from=6,
                              randomizationParams=randomizationParams,
                              statistic='median',N=100)

AnnaLaddach/TrajectoryGeometry documentation built on Feb. 23, 2024, 2:24 p.m.