Runtricycle: Run estimate_cycle_position on a Seurat object

In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object

Run estimate_cycle_position on a Seurat object

Description

This function run estimate_cycle_position function on Seurat object. It uses the tricycle internal reference projection matrix.

Usage

Runtricycle(
  object,
  assay = NULL,
  slot = "data",
  reduction.name = "tricycleEmbedding",
  reduction.key = "tricycleEmbedding_",
  gname = NULL,
  gname.type = c("ENSEMBL", "SYMBOL"),
  species = c("mouse", "human"),
  AnnotationDb = NULL,
  center.pc1 = 0,
  center.pc2 = 0
)

Arguments

object	Seurat object
assay	Assay to use, defaults to the default assay
slot	Slot to use. It should be library size adjusted **log-expression** values. Note that it is convention that we rename "logcounts" to "data" when converting SingleCellExperiment to Seurat object. See also as.Seurat. Defaults to "data"
reduction.name	Name of the cell cycle projection returned
reduction.key	Key for the cell cycle projection returned
gname	Alternative rownames of object. If provided, this will be used to map genes within object with genes in reference. If not provided, the rownames of object will be used instead. Default: NULL
gname.type	The type of gene names as in gname or rownames of object. It can be either 'ENSEMBL' or 'SYMBOL'. Default: 'ENSEMBL'
species	The type of species in object. It can be either 'mouse' or 'human'. Default: 'mouse'
AnnotationDb	An AnnotationDb objects. If the user provides rownames in the format of Ensembl IDs and project human data, this object will be used to map Ensembl IDs to gene SYMBOLs. If no AnnotationDb object being given, the function will use org.Hs.eg.db.
center.pc1	The center of PC1 when defining the angle. Default: 0
center.pc2	The center of PC2 when defining the angle. Default: 0

satijalab/seurat-wrappers documentation built on April 10, 2024, 3:25 p.m.