combine_cds: Combine a list of cell_data_set objects

In cole-trapnell-lab/monocle3: Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

Combine a list of cell_data_set objects

Description

This function will combine a list of cell_data_set objects into a new cell_data_set object.

Usage

combine_cds(
  cds_list,
  keep_all_genes = TRUE,
  cell_names_unique = FALSE,
  sample_col_name = "sample",
  keep_reduced_dims = FALSE
)

Arguments

cds_list	List of cds objects to be combined.
keep_all_genes	Logical indicating what to do if there is a mismatch in the gene sets of the CDSs. If TRUE, all genes are kept and cells from CDSs missing a given gene will be filled in with zeroes. If FALSE, only the genes in common among all of the CDSs will be kept. Default is TRUE.
cell_names_unique	Logical indicating whether all of the cell IDs across all of the CDSs are unique. If FALSE, the CDS name is appended to each cell ID to prevent collisions. These cell IDs are used as count matrix column names and colData(cds) row names. Cell names stored in other cds locations are not modified so you will need to modify them manually for consistency. Default is FALSE.
sample_col_name	A string to be the column name for the colData column that indicates which original cds the cell derives from. Default is "sample".
keep_reduced_dims	Logical indicating whether to keep the reduced dimension matrices. Default is FALSE.

Value

A combined cell_data_set object.

cole-trapnell-lab/monocle3 documentation built on April 7, 2024, 9:24 p.m.