Overview
QTLretrievR is an integration of qtl2 and intermediate to:
- map genotypes to probes (genoprobs)
- calculate Quantitative Trait Loci (QTL) peaks
- identify mediators of QTL peaks
- identify phenotypic effects within experimental data
The package is designed for use with experimental data from Diversity Outbred (DO) mice.
Getting started
Installation
QTLretrievR is not available on CRAN. To install, please use the instructions below:
remotes::install_github("deweyhannah/QTLretrievR")Please note that QTLretrievR has 2 Biocunductor packages as dependencies, they may not install if BiocManager is not available.
Submitting to a Job Scheduler
Currently, QTLretrievR is set up to identify available cores in a linux, mac, or windows environment. It is also able to identify the number of cores if you are submitting a job through a SLURM scheduler. Just make sure to include both of the following lines in your header:
#SBATCH --ntasks=N
#SBATCH --cpus-per-task=XWhen the number of cores is calculated for parallelization purposes, the total number of cores that are identified are N*X. If you don’t include both, and are submitting with a SLURM scheduler, it may not identify the correct number of cores.
If you are using any other scheduler, make sure that you specify the total number of cpus for the whole job. If applicable the number of processes should be 1.
Getting Help
If you find a clear bug, please file an issue with a minimal reproducible example on GitHub.