submit_jobs: Divide the entire data into many chunks submit...

In churchill-lab/scRATE: A Bayesian model selection approach to test zero inflation from scRNA-seq data

Description

Divide the entire data into many chunks submit "run_model_comparison" jobs on a pbs/torque cluster

Usage

submit_jobs(loomfile, num_chunks, outdir, dryrun, rfile, scriptfile,
  covariates = c(), layer = NULL, nCores = NULL, seed = NULL,
  gene_start = NULL, gene_end = NULL, chunk_start = NULL,
  chunk_end = NULL)

Arguments

loomfile	Expression quantity file (loom format)
num_chunks	Number of chunks
outdir	Name of the folder where results should be stored
dryrun	TRUE if you only want to check the job submission commands
rfile	R script to execute
scriptfile	PBS job submission script
covariates	Name of covariates (A col.attrs name in the input loomfile)
layer	Layer name of the count to use in the loom file
nCores	Number of cores to run stan fitting in parallel
seed	Seed number to reproduce randomized results
gene_start	Starting gene index to analyze
gene_end	Ending gene index to analyze
chunk_start	Starting chunk index to submit
chunk_end	Ending chunk index to submit

Value

... None is returned

churchill-lab/scRATE documentation built on Aug. 12, 2020, 2:52 p.m.