AJ partner project 2020
To develop an R package for testing the scope of applicability of different GWA methodologies, esp. with respect to varying: threshold between rare and common variants, the degree of contribution (effect size and direction) contributed by rare and common variants, degree of population structure, varying amount of contributing loci.
To use the package on Bianca:
gwasim package is automatically built into a docker container upon every push,
container is called gwasim-latest and is stored in
quiestrho account on DockerHub,
ssh to Rackham, do
singularity pull --docker-login docker://quiestrho/gwasim:latest
gwasim_latest.sif file into Bianca's wharf via sftp,
move the file from wharf to your project library,
singularity exec gwasim_latest.sif R --vanilla < script.r to run an R script within the container
The following input parameters are expected from the user: a VCF file with variants coming from a population under studies, a bed file containing a list of functional regions (e.g. gene list) along with their coordinates, a minor allele frequency threshold for cut-off between rare and common variants, the number of rare and common variants that contribute, distribution of effect sizes as a function of allele frequency (separately for the rare and the common alleles), percentage of alleles with negative effect (for both the common and the rare variants), parameters (mean, standard deviation) of the error term, type of the trait (continuous or binary, a cut-off value for the binary trait),
gwasimwith a VCF input is available here
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