add_seurat_clustering: add_seurat_clustering

In aertslab/SCopeLoomR: Build .loom files (compatible with SCope) and extract data from .loom files.

add_seurat_clustering

Description

Add all the Seurat clusterings in the given seurat object to the given .loom file handler.

Usage

add_seurat_clustering(
  loom,
  seurat,
  seurat.assay = "RNA",
  seurat.clustering.prefix = NULL,
  seurat.markers.file.path.list = NULL,
  seurat.marker.metric.accessors = NULL,
  seurat.marker.metric.names = NULL,
  seurat.marker.metric.description = NULL,
  default.clustering.resolution = NULL,
  default.clustering.overwrite = NULL,
  annotation = NULL,
  annotation.cluster.id.cn = NULL,
  annotation.cluster.description.cn = NULL
)

Arguments

loom	The loom file handler.
seurat	The Seurat object
seurat.assay	The assay to access the data from (only if you're using Seurat version 3). Option used only for sanity checks.
seurat.markers.file.path.list	The named list of file paths to the markers saved in RDS format. The names should be the resolution id of the corresponding clustering (e.g.: res.2). Default is NULL.
default.clustering.resolution	The clustering resolution (i.e.: res.2, ...) of the clustering that should be set as the default which an annotation can be set for.
annotation	A data.frame with annotation for the clusters of the default clustering. Default is NULL.
annotation.cluster.id.cn	The column name to use for the IDs of the clusters found by the given clustering group. Default is NULL.
annotation.cluster.description.cn	The column name to use for the description of the clusters found by the given clustering group. Default is NULL.

aertslab/SCopeLoomR documentation built on April 19, 2022, 11:25 a.m.