merge_sds {condiments} | R Documentation

## Merge slingshots datasets

### Description

If trajectory inference needs to be manually done condition per condition, this allows to merge them into one. It requires manual mapping of lineages.

### Usage

    merge_sds(..., mapping, condition_id = seq_len(ncol(mapping)), scale = FALSE)

### Arguments

`...` | Slingshot datasets
`mapping` | a matrix, one column per dataset. Each row amounts to lineage mapping.
`condition_id` | A vector of condition for each condition. Default to integer values in order of appearance
`scale` | If TRUE (default), lineages that are mapped are scaled to have the same length.

### Details

The function assumes that each lineage in a dataset maps to exactly one lineage in another dataset. Anything else needs to be done manually.

### Value

A modified slingshot dataset that can be used for downstream steps.

### Examples

    data(list = 'slingshotExample', package = "slingshot")
    if (!"cl" %in% ls()) {
      rd <- slingshotExample$rd
      cl <- slingshotExample$cl
    }
    sds <- slingshot::slingshot(rd, cl)
    merge_sds(sds, sds, mapping = matrix(c(1, 2, 1, 2), nrow = 2))

[Package condiments version 1.0.0 Index]