slingshot_conditions {condiments}R Documentation

Refitting slingshot per condition

Description

Test whether or not slingshot should be fitted independently for different conditions or not.

Usage

slingshot_conditions(sds, ...)

## S4 method for signature 'SlingshotDataSet'
slingshot_conditions(sds, conditions, approx_points = 100, ...)

## S4 method for signature 'SingleCellExperiment'
slingshot_conditions(sds, conditions, approx_points = 100, ...)

## S4 method for signature 'PseudotimeOrdering'
slingshot_conditions(sds, conditions, approx_points = 100, ...)

Arguments

sds

A slingshot object already run on the full dataset. Can be either a SlingshotDataSet or a SingleCellExperiment object.

...

Other arguments passed to getCurves

conditions

Either the vector of conditions, or a character indicating which column of the metadata contains this vector.

approx_points

Passed to getCurves

Value

A list of SlingshotDataSet, one per condition.

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)
sdss <- slingshot_conditions(sds, condition)

[Package condiments version 1.0.0 Index]