process

Applies several processing steps to a single cell genomics object.

process(x, ...)

# S3 method for Seurat
process(
  x,
  assay = NULL,
  dims = 1:10,
  algorithm = 1,
  resolution = 0.6,
  nfeatures = 2000,
  metric = "cosine",
  n.neighbors = 30L,
  min.dist = 0.3,
  spread = 1,
  verbose = FALSE,
  ...
)

Arguments

x

an object of class Seurat.

...

arguments passed down to methods.

assay

assay to use for processing.

dims

PCA dimensions to use for UMAP and clustering.

algorithm

algorithm to use for clustering.

resolution

resolution to use for clustering.

nfeatures

number of features for FindVariableFeatures().

metric

metric used for UMAP.

n.neighbors

number of nearest-neighbors to use for UMAP.

min.dist

min.dist for UMAP.

spread

spread for UMAP.

verbose

whether to output diagnostic information.