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Step 1 of mcRigor two-step: Identifying the single cells that constitute dubious metacells and need to be re-partitioned.

mcRigorTS_Step1.Rd

Step 1 of mcRigor two-step: Identifying the single cells that constitute dubious metacells and need to be re-partitioned.

Usage

mcRigorTS_Step1(
  obj_singlecell,
  sc_membership,
  TabMC = NULL,
  method = c("seacells", "mc1", "mc2", "supercell", "metaq")
)

Arguments

obj_singlecell

A Seurat object of the original single cells.

sc_membership

A named vector (or dataframe) of the metacell membership of single cells.

TabMC

A dataframe containing the permutation results and mcRigor results in dubious metacell detection. Saved in the previous steps through function mcRigor_DETECT.

method

The metacell partitioning method used to build metacells. Available: "seacells" (default, SEACells), "mc1" (MetaCell), "mc2" (MetaCell2), "supercell" (SuperCell), "metaq" (MetaQ).

Value

A list containing the following fields:

obj_sc_dub

A Seurat object of single cells that are marked as dubious and will be re-partitioned.

target_res

A list containing the permutation results, derived thresholds, and mcRigor results in dubious metacell detection, given by function mcRigor_threshold.

obj_metacell_step1

The metacell object built under the membership sc_membership, with more dubious metacells marked.