scmat_read_scmat_10x: Read a matrix from the output of a 10x run. Batches can be...

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

Read a matrix from the output of a 10x run. Batches can be stripped from the cell identifier if in BARCODE-LANE format.

Description

Read a matrix from the output of a 10x run. Batches can be stripped from the cell identifier if in BARCODE-LANE format.

Usage

scmat_read_scmat_10x(
  matrix_fn,
  genes_fn,
  cells_fn,
  paralogs_policy = get_param("scm_10x_paralogs_policy"),
  use_batches = get_param("scm_10x_batches"),
  min_umis_n = get_param("scm_min_cell_umis"),
  dataset_id = "NS"
)

Arguments

matrix_fn	matrix input file name. Expecting a tab delimited file with 3 columns and a header: 'row', 'column', 'value'. row and column fields are the row and column matrix coordinates of the value.
genes_fn	linking to the rownames.tab
cells_fn	linking to the colnames.tab
paralog_policy	- how to treat entries with the same gene name. Currently supporting "sum" for adding up the umis and "remove" for removing the gene. TBA: "split".

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