progressionTest_multipleSamples: Differential Progression Test with multiple samples

In HectorRDB/condiments: Differential Topology, Progression and Differentiation

Differential Progression Test with multiple samples

Description

Test whether or not the pseudotime distribution are identical within lineages between conditions, with samples not being confounded by conditions

Usage

progressionTest_multipleSamples(pseudotime, ...)

## S4 method for signature 'matrix'
progressionTest_multipleSamples(
  pseudotime,
  cellWeights,
  conditions,
  Samples,
  ...
)

## S4 method for signature 'SlingshotDataSet'
progressionTest_multipleSamples(pseudotime, conditions, Samples, ...)

## S4 method for signature 'SingleCellExperiment'
progressionTest_multipleSamples(pseudotime, conditions, Samples, ...)

## S4 method for signature 'PseudotimeOrdering'
progressionTest_multipleSamples(pseudotime, conditions, Samples, ...)

Arguments

pseudotime	Can be either a SlingshotDataSet or a SingleCellExperiment object or a matrix of pseudotime values, each row represents a cell and each column represents a lineage.
...	Other arguments passed to progressionTest.
cellWeights	If 'pseudotime' is a matrix of pseudotime values, this represent the cell weights for each lineage. Ignored if 'pseudotime' is not a matrix.
conditions	Either the vector of conditions, or a character indicating which column of the metadata contains this vector.
Samples	A vector assigning each cell to a sample. Samples must be shared across all conditions.

Value

The same object has the progressionTest with one more column per sample.

Examples

data('slingshotExample', package = "slingshot")
rd <- slingshotExample$rd
cl <- slingshotExample$cl
condition <- factor(rep(c('A','B'), length.out = nrow(rd)))
condition[110:139] <- 'A'
sds <- slingshot::slingshot(rd, cl)
samples <- sample(1:2, 140, replace = TRUE)
progressionTest_multipleSamples(pseudotime = sds, conditions = condition, Samples = samples)

HectorRDB/condiments documentation built on Feb. 5, 2024, 10:24 p.m.