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ReadVelocity() reads a .loom file produced by velocyto and returns a list of spliced, unspliced, and ambiguous count matrices that can be loaded into Seurat.

​
Syntax

ReadVelocity(
  file,
  engine = "hdf5r",
  verbose = TRUE
)

​
Parameters

​
file
character
required
Path to the .loom file generated by velocyto.
​
engine
character
default:"hdf5r"
HDF5 reading engine to use. Options: "hdf5r" or "rhdf5". Passed to velocyto.R::read.loom.matrices().
​
verbose
logical
default:"TRUE"
Print progress messages from velocyto.R.

​
Returns

A named list of sparse matrices:
  • spliced — spliced RNA counts
  • unspliced — unspliced (nascent) RNA counts
  • ambiguous — ambiguously spliced counts
Use as.Seurat() on this list to create a Seurat object with three separate assays.

​
Prerequisites

remotes::install_github("velocyto-team/velocyto.R")

​
Examples

library(SeuratWrappers)

# Read velocity data
ldat <- ReadVelocity(file = "sample.loom")

# Convert to Seurat with three assays: spliced, unspliced, ambiguous
object <- as.Seurat(ldat)

# Set spliced as default and preprocess
DefaultAssay(object) <- "spliced"
object <- SCTransform(object)
object <- RunPCA(object)
object <- RunUMAP(object, dims = 1:30)

# Then run velocity estimation
object <- RunVelocity(object = object, reduction = "pca", ncores = 8)

​
See Also

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