mc_build_cgraph: Builds cell graph object using Metacell package

In mariiabilous/SuperCellBM:

Description

Builds cell object of Metacell package using UMI data. No gene filtering performed inside, so either provide ge.mtrx as a UMI matrix with row containing only genes of interest or specify which genes to use via genes.to.use

Usage

mc_build_cgraph(
  ge.mtrx,
  k.knn,
  genes.to.use = NULL,
  T_vm = -Inf,
  project_name = "metacell",
  balanced.Knn = TRUE,
  return.igraph = TRUE,
  verbose = FALSE,
  force_mcell_add_gene_stat = TRUE
)

Details

@param ge.mtrx UMI matrix with genes stored as rows, cells stored as cols @param k.knn k-kearest neighbors parameter (should be large (~100) if cgraph is balanced) @param genes.to.use vector of genes to use for building cgraph. If NULL (default), all the genes from ge.mtrx will be used @param T_vm min variance of geness to keep for MC construction (default is -Inf - no MC gene filtering) @param project_name used for storing and accessing .Rda files of Metacell output @param balanced.Knn whether cgraph have to be computed using balanced kNN from Metacell package (keep k.knn large then (~100)) @param return.igraph whether to return igraph object of cgraph

@return mat – mat object of metacell @return mat_name – name of mat object @return gstat – gstat oject of metacell @return gstat_name – name of gstat object @return gset – gset oject of metacell @return gset_name – name of gset object @return cgraph – cgraph oject of metacell @return cgraph_name – name of cgraph object ' @return ograph – igraph object of cgraph (if return.igraph == TRUE) @return k.knn – k.knn input parameter @return balanced.Knn – balanced.Knn input parameter @return project.name – project.name parameter

mariiabilous/SuperCellBM documentation built on Jan. 28, 2022, 7:45 p.m.