analyseSingleCellTrajectory: Analyse a single cell trajectory.

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

Analyse a single cell trajectory.

Description

This function analyses a single cell trajectory by sampling multiple paths and comparing each path to random paths. It takes vector of pseudotime values, and a matrix of attribute values (cell x attribute). It also optionally takes the number of pseudotime windows to sample a single cell from. This defaults to 10. The function returns a list of Answers for each comparison of a sampled path to a random path.

Usage

analyseSingleCellTrajectory(
  attributes,
  pseudotime,
  randomizationParams,
  statistic,
  nSamples = 1000,
  nWindows = 10,
  d = ncol(attributes),
  N = 1000
)

Arguments

attributes	- An n x d (cell x attribute) matrix of numeric attributes for single cell data. Rownames should be cell names.
pseudotime	- A named numeric vector of pseudotime values for cells.
randomizationParams	- A character vector which is used to control the production of randomized paths for comparison.
statistic	- Allowable values are 'median', 'mean' or 'max'.
nSamples	- The number of sampled paths to generate (default 1000).
nWindows	- The number of windows pseudotime should be split into to sample cells from (defaults to 10).
d	- The dimension under consideration. This defaults to ncol(attributes).
N	- The number of random paths to generated for statistical comparison to the given path (defaults to 1000).

Value

This returns a list, where each entry is itself a list containing information comparing a sampled path to random paths. These entries consist of: 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

chol_answers = analyseSingleCellTrajectory(chol_attributes[,seq_len(3)],
                                         chol_pseudo_time_normalised,
                                         nSamples = 10,
                                         randomizationParams =
                                                     c('byPermutation',
                                                   'permuteWithinColumns'),
                                         statistic = "mean",
                                         N = 1)
hep_answers = analyseSingleCellTrajectory(hep_attributes[,seq_len(3)],
                                         hep_pseudo_time_normalised,
                                         nSamples = 10,
                                         randomizationParams =
                                                   c('byPermutation',
                                                   'permuteWithinColumns'),
                                         statistic = "mean",
                                         N = 1)

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