performUMAP: Perform UMAP dimensionality reduction on SingleCellExperiment...
In kordastilab/ImmunoCluster: Fast and accesible Immune profiling CyTOF data

Description Usage Arguments Value Author(s) Examples

Perform UMAP dimensionality reduction on SingleCellExperiment object

performUMAP(
  indata,
  assay = "scaled",
  downsample = NULL,
  downsample_grouping = "group",
  reducedDim = NULL,
  dims = seq_len(20),
  newDimName = NULL,
  useMarkers = NULL
)

`indata`	a `SingleCellExperiment`.
`assay`	the SCE assay to choose from.
`downsample`	a numeric of the number of cells to downsample by.
`downsample_grouping`	a character string indicating which metadata grouping to downsample by.
`reducedDim`	a character vector represting a dimensionality reduction slot from the SCE to be selected as input data.
`dims`	numeric of reduced dimensions to select from the reducedDim
`newDimName`	character string of the name for the resulting UMAP dimensionality reduction in the SCE object.
`useMarkers`	chacter vector of markers to use as input for the UMAP run.

a SingleCellExperiment object.

Kevin Blighe, James Opzoomer james.opzoomer@kcl.ac.uk

# Download complete ImmunoCluster SCE object from zenodo
sce_gvhd = readRDS(url("https://zenodo.org/record/3801882/files/sce_gvhd.rds"))

# Run UMAP and store in sce object
sce_gvhd = performUMAP(sce_gvhd)