analyseBranchPoint {TrajectoryGeometry} | R Documentation

## Analyse branch point.

### Description

This function takes a single cell trajectory and analyses it starting from successively later points in pseudotime, with the rationale that a more consistent directionality will be followed after the branch point.

### Usage

    analyseBranchPoint(
    attributes,
    pseudotime,
    randomizationParams,
    statistic,
    start = (max(pseudotime) - min(pseudotime)) * 0.25,
    stop = (max(pseudotime) - min(pseudotime)) * 0.75,
    step = (max(pseudotime) - min(pseudotime)) * 0.05,
    nSamples = 1000,
    nWindows = 10,
    d = ncol(attributes),
    N = 1
    )

### 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'.
`start` | - The first pseudotime value (percentage of the trajectory) from which to analyse the trajectory from. Defaults to 25% of the way through the trajectory.
`stop` | - The last pseudotime value (as a percentage of the trajectory) from which to analyse the trajectory from. Defaults to 75% of the way through the trajectory.
`step` | - The size of the step to take between successively later starting points in pseudotime. Defaults to 5% of the trajectory length.
`nSamples` | - The number of sampled paths to generate (defaults to 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 of results for analyseSingleCellTrajectory, named by trajectory starting point. Each result from analyseSingleCellTrajectory is a list which contains an entry for each sampled path. Each of these entries is a list containing information comparing the sampled path in question to random paths. The 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_branch_point_results = analyseBranchPoint(chol_attributes[,seq_len(3)],
                            chol_pseudo_time[!is.na(chol_pseudo_time)],
                            randomizationParams = c('byPermutation',
                                            'permuteWithinColumns'),
                            statistic = "mean",
                            start = 0,
                            stop = 50,
                            step = 5,
                            nSamples = 10,
                            N = 1)

[Package TrajectoryGeometry version 1.0.0 Index]