combine_cds: Combine a list of cell_data_set objects

View source: R/utils.R

combine_cdsR Documentation

Combine a list of cell_data_set objects


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


  keep_all_genes = TRUE,
  cell_names_unique = FALSE,
  sample_col_name = "sample",
  keep_reduced_dims = FALSE



List of cds objects to be combined.


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.


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.


A string to be the column name for the colData column that indicates which original cds the cell derives from. Default is "sample".


Logical indicating whether to keep the reduced dimension matrices. Default is FALSE.


A combined cell_data_set object.

cole-trapnell-lab/monocle3 documentation built on May 24, 2022, 5:25 p.m.