mcell_pipe_mat2mc2d: Linear simple pipeline for turning a matrix to a MC and...

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

Linear simple pipeline for turning a matrix to a MC and plotting std figs

Description

The simplification here is that all objects (mat, gstat, marker gset, cgraph, coclust, mc, mc2d) will have the same ID and will be produced linerly without much questions asked. Also the parameters are simplified for typical use in small datasets.

Usage

mcell_pipe_mat2mc2d(
  mat_id,
  T_vm = 0.2,
  T_tot = 200,
  T_top3 = 3,
  Knn = 120,
  n_resamp = 500,
  T_weight = round(n_resamp * 0.75/8)
)

Arguments

mat_id	the id to start from
T_vm	threshold on normalized varmin, for selecting markers. Lower this is you don't get enough info from the selected markers. (0.2)
T_tot	threshold on minimal total expression for markers (200)
T_top3	threshold on minimal number of genes in the top3 expressing cells for markers (3)
Knn	the raw Knn parameter used for constructing a balanced Knn graph. This should be set to roughly the size of desired metacells (120)
n_resamp	number of bootstraps (500). Decrease to save time.
T_weight	number of co-clustering occurences in bootstrap to add an edge in the phase of generating metacells from the bootstrap co-clustering matrix.

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