perform.slingshot.trajectory: Performs Slingshot trajectory inference

In connorhknight/IBRAP: Integrated Benchmarking scRNA-seq Analytical Pipeline (IBRAP)

Performs Slingshot trajectory inference

Description

Generates slingshot trajectory inference on the defined reduction and clustering

Usage

perform.slingshot.trajectory(
  object,
  reduction,
  assay,
  clust.method,
  column,
  start.clus = NULL,
  end.clus = NULL,
  verbose = FALSE,
  seed = 1234,
  ...
)

Arguments

object	IBRAP S4 class object
reduction	Character. String defining which reduction to supply to the clustering algorithm. Default = NULL
assay	Character. String containing indicating which assay to use
clust.method	Character. Which cluster method should be used utilised from clustering results, if ''metadata'' is supplied, you will access the metadata.
column	Character. Which column within the isolated clust.method should be used to define cell type annoation.
start.clus	Character. Which cluster should start the trajectory, if NULL then slingshot will attempt to discover this. Default = NULL
end.clus	Character. Which cluster should end the trajectory, if NULL then slingshot will attempt to discover this. Default = NULL
verbose	Logical Should function messages be printed?
seed	Numeric. What should the seed be set as. Default = 1234
...	arguments to be passed to slingshot::slingshot

Value

A SingleshotDataSet class results object containing cellular lineages/curves

Examples

traj_res <- perform.slingshot.trajectory(object = object, reduction = 'pca_umap', 
                                         assay = 'SCT', clust.method = 'metadata', 
                                         column = 'celltype')
                                         
plot.slingshot(result = traj_red, object = traj, assay = 'SCT', relevant = F, Pseudotime = T)

connorhknight/IBRAP documentation built on March 9, 2023, 7:01 p.m.