read_velocity_output: Read intronic and exonic matrices into R

In lambdamoses/BUStoolsR: kallisto | bustools R utilities

Read intronic and exonic matrices into R

Description

Read intronic and exonic matrices into R

Usage

read_velocity_output(spliced_dir, unspliced_dir, spliced_name, unspliced_name)

Arguments

spliced_dir	Directory with mtx file for UMI counts of spliced transcripts.
unspliced_dir	Directory with mtx file for UMI counts of unspliced transcripts.
spliced_name	The files in the splicedd directory should be <spliced_name>.mtx, <spliced_name>.genes.txt, and <spliced_name>.barcodes.txt.
unspliced_name	The files in the unsplicedd directory should be <unspliced_name>.mtx, <unspliced_name>.genes.txt, and <unspliced_name>.barcodes.txt.

Value

A list of two dgCMatrix with barcodes as column names and genes as row names. The elements of the list will be spliced and unspliced.

Examples

# Internal toy data used for unit testing
toy_path <- system.file("testdata", package = "BUSpaRse")
m <- read_velocity_output(toy_path, toy_path,
  spliced_name = "genes",
  unspliced_name = "genes")

lambdamoses/BUStoolsR documentation built on Aug. 1, 2024, 6:30 a.m.