RunSlingshot: Returns a slingshot based on the plsda of a seurat object

In sbrn3/disscat: Calculates Distances Between Single Cell RNA Seq Categories

Description

Returns a slingshot based on the plsda of a seurat object

Usage

RunSlingshot(seurat_object, reduction, dims = 1:2,
  group.by = "recluster", output = "seurat", thresh = 0.001)

Arguments

seurat_object	seurat_object containing counts and metadata
reduction	Dimensionality reduction data to use
dims	Dimensions to use
group.by	Categories that it will draw trajectories through. If there is no preference then it is possible to select "recluster" where it will cluster cells and generate groups using Mclust.
output	Output object. Can choose "sce"(Single Cell Experiment S4), "slingshot" (Slingshot S4) or "seurat"(Seurat S4)

Value

a sce which contains the slingshot data

sbrn3/disscat documentation built on Dec. 12, 2019, 7:54 a.m.