Interoperability with other scRNA formats

Yaniv Lubling

13-02-2019

Metacell supports conversion of the umi matrix object to/from Bioconductor's SingleCellExperiment object (a format that can be imported into Seurat).

Convert a metacell umi matrix object to a SingleCellExperiment object

The export function creates a SingleCellExperiment object and stores in it the raw umi counts and the metadata data.frame. The function expects the ID of the mat object to be exported:

sce = scm_export_mat_to_sce(mat_id)

If you wish to import the SingleCellExperiment object into Seurat you should also export the log-normalized umi matrix (and then specify the number of umis to scale each cell to before taking the log).

sce = scm_export_mat_to_sce(mat_id, add_log_counts=TRUE, scale_to=10000)

# To convert the sce into a Seurat object (Seurat v2.0):
# library(Seurat)
# seurat_obj = Convert(sce, to="seurat")

Convert a SingleCellExperiment object into a metacell umi matrix one

The import function expects a SingleCellExperiment object with the raw umi counts in an assay named "counts" (can be changed by the counts_slot parameter) and it also imports the cells metadata table:

mat = scm_import_sce_to_mat(sce)

# The sce object can be converted from a Seurat object:
# libray(Seurat)
# sce = Convert(seurat_obj, "sce")