mcell_import_scmat_tsv: Load a matrix from a simple dense table with genes in rows...

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

Load a matrix from a simple dense table with genes in rows and cells in columns. First column is the gene name

Description

Load a matrix from a simple dense table with genes in rows and cells in columns. First column is the gene name

Usage

mcell_import_scmat_tsv(
  mat_nm,
  fn,
  genes_fn = NULL,
  meta_fn = NULL,
  dset_nm = NULL,
  force = FALSE,
  paralogs_policy = "sum"
)

Arguments

mat_nm	- the name of the new matrix in scdb
fn	path of the matrix to read (columns names should represent Cell.IDs, rownames should represent gene names, values are expected to represent number of UMIs per gene per Cell)
meta_fn	meta data table to read. If this is null, all cells will be onsidred as part of a single Amp.Batch and Dataset.ID. The table must include at least the fields "Cell.ID", "Amp.Batch.ID", "Seq.Batch.ID", "Batch.Set.ID", where Cell.ID should match the names of cells in the data matrix.
force	- if true, will import from 10x files even when the matrix is present in the DB

tanaylab/metacell documentation built on Jan. 29, 2025, 1:34 a.m.