mcell_mc_split_filt: Split and filter metacells using dbscan and outlier gene...
In tanaylab/metacell: Meta cell analysis for single cell RNA-seq data

mcell_mc_split_filt

R Documentation

Split and filter metacells using dbscan and outlier gene detection

Description

Running intra-metacell clustering on each metacell, identifying splits if existing. Also remove cells with outlier expression from each metacell. Note that this can in many case eliminate doublets as outliers - but may be insffucieint as doublets may constitute homogeneous metacells in large datasets.

Usage

mcell_mc_split_filt(
  new_mc_id,
  mc_id,
  mat_id,
  T_lfc,
  plot_mats = T,
  dirichlet = F
)

Arguments

`new_mc_id`	id of metacells to create
`mc_id`	id of source metacell object
`mat_id`	id of umi matrix
`plot_mats`	if this is true, a heatmap will be generated for each metacell
`dirichlet`	if this is true, the distance metric to be used for splitting is dirichlet on the downsampled umi counts. Otherwise (and by default), the correlation between log(1+umi) of the downsampled matrix will be used. Note that downsampling is done given the miminum depth of each metacell, seperately.