mcatlas_annotate_mc_by_sc2sc_projection: Annotate query metacell with atlas by comparing query cells...

In tanaylab/metacell: Meta cell analysis for single cell RNA-seq data

Annotate query metacell with atlas by comparing query cells to altas cells with a Knn strategy Algorithm short description TBA

Description

Annotate query metacell with atlas by comparing query cells to altas cells with a Knn strategy Algorithm short description TBA

Usage

mcatlas_annotate_mc_by_sc2sc_projection(
  atlas_id,
  qmc_id,
  qmat_id,
  qmat_naming_type,
  all_vs_all,
  new_qmc_id,
  T_cor_gap = 1,
  fig_cmp_dir = NULL,
  sc_annots = NULL
)

Arguments

atlas_id	id of atlas object in scdb
qmc_id	id of metacell object ina scdb
qmat_id	id of query umi matrix
qmat_naming_type	naming scheme of query matrix/mc
all_vs_all	should a graph combining query and atlas be constructed, or only K-nn of a bipartiate query atlas graph be examined.
new_qmc_id	id of recolored metacell object to save in DB (NULL will supress updating db)
T_cor_gap	how much gap between internal atlas mc-mc correlation and query-atlas correlation one is allowing to keep the annotation.
fig_cmp_dir	name of directory to put figures per MC
sc_annot	cached sc_annot object can be specified (as returned by mcatlas_annotate_sc_by_projection) - to save time in repeated annotation refinement

tanaylab/metacell documentation built on Oct. 19, 2023, 1:01 p.m.