read_mtx: Read a trio of genes, barcodes and mtx files.

In jmonlong/scCNAutils: Functions to analyze copy number aberrations in single-cell data

Read a trio of genes, barcodes and mtx files.

Description

Read a trio of genes, barcodes and mtx files.

Usage

read_mtx(
  mtx_file = "matrix.mtx",
  genes_file = "genes.tsv",
  barcodes_file = "barcodes.tsv",
  path = ".",
  rm_dup = TRUE,
  genes_col = 2,
  min_barcode_exp = 1,
  filter_zero_genes = TRUE
)

Arguments

mtx_file	the path to the mtx file
genes_file	the path to the genes file.
barcodes_file	the path to the barcodes file
path	the path to the folder containing the files
rm_dup	remove duplicated gene names? Default is TRUE.
genes_col	the column to use in genes_file. Default is 2.
min_barcode_exp	minimum total expression in barcodes/cells. Default is 1.
filter_zero_genes	filter genes with no reads in any cells? Default is TRUE.

Value

a data.frame with a 'symbol' column with gene names and one column per barcode.

Author(s)

Jean Monlong

jmonlong/scCNAutils documentation built on Feb. 8, 2025, 8:09 a.m.