process: process

In ddiez/scmisc: Miscellaneus Tools for the Analysis of Single Cell Data

process

Description

Applies several processing steps to a single cell genomics object.

Usage

process(x, ...)

## S3 method for class '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.

ddiez/scmisc documentation built on July 21, 2024, 11:35 a.m.