samplePath: Sample a path from single cell data

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

Sample a path from single cell data

Description

This function 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 matrix of sampled attribute values which form the coordinates of the sampled path. The matrix of attribute values should consist of numeric values relevant to a pseudotime trajectory i.e. gene expression values or PCA projections. The vector of pseudotime values should be named according to cell names. Simarly the row names of the matrix of attribute values should be cell names. Row names for the returned matrix of the sampled path give the window number a cell was sampled from.

Usage

samplePath(attributes, pseudotime, nWindows = 10)

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.
nWindows	- The number of windows pseudotime should be split into to sample cells from. Defaults to 10.

Value

sampledPath - A path consisting of a matrix of attributes of sampled cells. The rownames refer to the pseudotime windows cell was sampled from.

Examples

samplePath(chol_attributes, chol_pseudo_time_normalised)
samplePath(hep_attributes, hep_pseudo_time_normalised)

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