read_velocity_output: Read intronic and exonic matrices into R

Description Usage Arguments Value Examples

View source: R/utils.R

Description

Read intronic and exonic matrices into R

Usage

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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

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# 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 June 9, 2021, 6:15 p.m.