rest2api

A Docker image for use with qtl2api.

Building

docker build --progress plain -t churchilllab/qtl2rest .

Running

The Docker image needs a file and a path to be mounted in the following loctions:

/app/qtl2rest/data

• R data directory - this should have RData and Rds files

ccfoundersnps.sqlite

• founder snps database

The following command will start the Docker image.

    docker run --rm \
        -p 8001:8001 \
        --name qtl2rest \
        --network qtl2rest \
        -v /data/rdata:/app/qtl2rest/rdata \
        -v /data/ccfoundersnps.sqlite:/app/qtl2rest/data/ccfounders.sqlite -v \
        churchilllab/qtl2rest

API

The following API Endpoints will be available:

/envinfo

• Get information about the files loaded and what elements they contain

/markers

• Get all the markers or markers for a chromosome

/datasets

• Get information about the datasets loaded

/datasetsstats

• Get statistic information about the datasets loaded

/rankings

• Get a ranking of gene annotations. For use with SNP association.

/idexists?id={id}&dataset={dataset}

• See if the id exists in the viewer or dataset if dataset is supplied.

/lodpeaks?dataset={dataset}

• Get LOD peaks for the specified dataset.

/lodscan?dataset={dataset}&id={id}&intcovar={covar}

• Perform a LOD scan on the id in the dataset. An optional interactive covariate can be specified (covar).

/lodscansamples?dataset={dataset}&id={id}&chrom={chromosome}&intcovar={covar}

• Perform a LOD scan on the id in the dataset for a specific chromosome. An interactive covariate must be specified (covar). This will group samples by the covar and return a LOD scan for each unique covar value.

/expression?dataset={dataset}&id={id}

• Get the expression data for the id in the dataset.

/snpassoc?dataset={dataset}&id={id}&chrom={chromosome}&location={location}&window_size={windowSize}

• Perform a SNP association mapping for the specified id, dataset, chromsome, location, and windowSize.

/mediate?dataset={dataset}&id={id}&marker_id={markerID}&dataset_mediate=${dataset_mediate}

• Perform a mediation scan for the specified id, dataset, and markerID. If dataset_mediate is specified, the mediation will be against that dataset.

/foundercoefs?dataset={dataset}&id={id}&chrom={chromosome}&intcovar={covar}

• Get the Founder coefficient data or the specified id, dataset, and markerID. If covar is specified, that interactive covariate will be used.

/correlation?dataset={dataset}&id={id}&dataset_correlate={dataset_correlate}&intcovar={covar}

• Perform a correlation scan for the specified id in dataset. If dataset_correlate is specified, the correlation will be against that dataset. If covar is specified, that interactive covariate will be used.

/correlationplot?dataset={dataSet}&id={id}&dataset_correlate={dataset_correlate}&id_correlate={id_correlate}&intcovar={covar}

• Perform a correlation scan for the specified id in dataset against the specified id_correlate in dataset_correlate. If covar is specified, that interactive covariate will be used. This is mainly for seeing how the two ids look when plotted.