r_make_loom_files: Wrapper to Make Loom Files in R

In kidcancerlab/rrrSingleCellUtils: A Set of Tools For Single Cell Analysis

Wrapper to Make Loom Files in R

Description

Wrapper to Make Loom Files in R

Usage

r_make_loom_files(
  input_table,
  out_dir = "loom_output/samples",
  cluster_account,
  slurm_base = paste0(getwd(), "/slurmOut"),
  sbatch_base = "sbatch_"
)

Arguments

input_table	Dataframe or tibble with columns titled "sample_id", "h5_path", "bam_path", and "gtf_path"
out_dir	Folder to output loom files and sbatch output to. By default will create a directory in your working directory called loom_output/samples. Each sample_id found in input_table will have its own directory within out_dir
cluster_account	Your Franklin cluster user ID.
slurm_base	The directory to write slurm output files to.
sbatch_base	The prefix to use with the sbatch job file.

Details

This is a wrapper function around velocyto's "run" command. It will take a table of sid's and other info and create loom files based on all cells that are in the h5 object. The loom files can then be used to run velocity analysis using scVelo. Slurm error and std output will be written to out_dir/sample_id/.

Value

A loom file for each unique ID present in id_col, output to loom_dir.

kidcancerlab/rrrSingleCellUtils documentation built on April 17, 2025, 5:10 p.m.