Example/README.md

In wanyuac/GeneMates: Analysing association and physical linkage between bacterial genes

Demonstration

Users may follow this tutorial to see the performance and output of the function findPhysLink performs.

Data set

The test data were derived from an Escherichia coli data set published by D. Ingle et al. and can be downloaded (DOI: 10.26188/5cbd1f18b2602) from a FigShare server maintained by the University of Melbourne.

Citation: Ingle, D. J. et al. Evolution of atypical enteropathogenic E. coli by repeated acquisition of LEE pathogenicity island variants. Nat. Microbiol. 1, 15010 (2016).

Procedure

When SLURM Workload Manager is used, please specify arguments indicated by square brackets in the following SLURM scripts before running the scripts.

sbatch findPhysLink.slurm  # to produce a linkage network
sbatch lmm.slurm  # to produce an association network

Users can also launch local runs with R commands:

Rscript --vanilla findPhysLink.R  # to produce a linkage network
Rscript --vanilla lmm.R  # to produce an association network

Script process_results.R shows basic commands for processing GeneMates outputs.

Results

Outputs from findPhysLink for two runs (with and without allelic physical distances) are archived and compressed into file Output.tar.gz (DOI: 10.26188/5cbd22cd00780), which can be downloaded from the FigShare server as well. Since the LMM-only run (without physical distances) shares most of its outputs with the full run (with physical distances), only the result file lmm.rds is included in Output.tar.gz.

Output: the directory for GeneMates outputs for the test data set

• lmm.rds: produced with lmm.slurm.
• findPhysLink: a directory containing complete results of findPhysLink.slurm.
• physlink.rds: evidence of physical linkage.
• snps.rds (processed SNP tables), which is the same as that produced by lmm.slurm.

wanyuac/GeneMates documentation built on Aug. 12, 2022, 7:37 a.m.