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QTL Viewer

This is a web application that renders QTL "type" data. There are multiple components and moving parts, but 2 different main projects make up the QTL Viewer: QTL API and QTL Web.

QTL API

Overview

Docker and Docker Compose are the recommended way of running the QTL API so it can be easily managed. A Docker image for the QTL API can be found on Docker Hub at mattjvincent/rqtlapi.

This image contains all the necessary code to run the QTL API. An example docker-compose.yml can be found in the churchill-lab/qtlapi GitHub repository.

An example to start this Docker image is:

docker run --rm -p 8000:8000 --network netapi \
           -v /path/to/my.RData:/app/qtlapi/data/data.RData \
           -v /path/to/ccfoundersnps.sqlite:/app/qtlapi/data/ccfounders.sqlite \
           -v /path/to/qtlapi.R:/app/qtlapi/qtlapi.R \
           mattjvincent/qtlapi /app/qtlapi/qtlapi.R

For more in depth documentation, please refer to churchill-lab/qtlapi.

Tech Stack

  • Docker - Build, Ship, and Run Any App, Anywhere
  • R - number cruncher
  • R/qtl2 - Analysis
  • Plumber - Help turn R code into Web based API

Data

Behind the QTL API is a RData file which MUST be formatted according to the following definition: QTL API Data File Definition

Endpoints

The API generated is used by the QTL Web app. The following API's are supplied:

/datasets

Description: This is the initial API called by QTL Web. The data returned is dependent upon if the dataType is mRNA, protein, or phenotype. The purpose of this API is to define and describe the datasets used in the viewer.

Parameters: None

Response: The response will be JSON.

Example response:

{"dataSets": [{
    "id": "some.dataset.identifier",
    "displayName": "Some Dataset",
    "dataType": "mRNA",
    "gene_ids": [
         "ENSMUSG00000000001",
         "ENSMUSG00000000028",
         "ENSMUSG00010203821",
         ...
    ],
    "protein_ids": [],
    "phenotypes" : [],
    "covarFactors":[{
        "column.name":"sex",
        "display.name":"Sex"
    }, {
        "column.name":"gen",
        "display.name":"Generation"}]
    },
    ...
    ],
    "ensemblVersion": 75,
    "numMarkers": 68433    
}

/lodscan

Description: Perform a LOD Scan.

Parameters:

Parameter Description
dataset dataset identifier
id the identifer to perform LOD scan on
regressLocal TRUE to regress on local genotype, FALSE to not
nCores number of cores to use
expand TRUE to expand the JSON, FALSE to condense

Response: The response will be JSON.

Example Response:

{"result": [
    {"id":"1_4530778","chr":"1","pos":4.5308,"lod":1.688},
    {"id":"1_4533435","chr":"1","pos":4.5334,"lod":1.6709},
    ...
    {"id":"1_4536092","chr":"1","pos":4.5361,"lod":1.6539}
],
 "time":5.3
}

/foundercoefs

Description: Get founder coefficients.

Parameters:

Parameter Description
dataset dataset identifier
id the identifer to perform LOD scan on
chrom the chromosome
regressLocal TRUE to regress on local genotype, FALSE to not
blup TRUE to perform Best Linear Unbiased Predictors
center TRUE to center around 0
nCores number of cores to use
expand TRUE to expand the JSON, FALSE to condense

Response: The response will be JSON.

Example Response:

{"result":[{"id":"2_4292516","chr":"2","pos":4.2925,
            "A":0.012,"B":-0.0267,"C":0.0345,"D":0.1994,
            "E":0.1305,"F":-0.4769,"G":0.1217,"H":0.0055},
           {"id":"2_4337139","chr":"2","pos":4.3371,
            "A":0.0114,"B":-0.0267,"C":0.0343,"D":0.2,
            "E":0.1307,"F":-0.4769,"G":0.1218,"H":0.0055},
            ...
           {"id":"2_4369263","chr":"2","pos":4.3693,
            "A":0.012,"B":-0.0259,"C":0.0407,"D":0.2006,
            "E":0.1323,"F":-0.4783,"G":0.1134,"H":0.0052}
        ],
 "time":2.3
}

/expression

Description: Get the expression data.

Parameters:

Parameter Description
dataset dataset identifier
id the identifer to perform LOD scan on

Response: The response will be JSON.

Example Response:

{"data":[{"mouse_id":"F01","Sex":"F","Generation":"G4","Litter":2,
          "Diet":"hf","Coat.Color":"agouti","GenerationLitter":"G4_2",
          "expression":0.2243,"_row":"F01"},
          ...
         {"mouse_id":"F02","Sex":"F","Generation":"G4","Litter":2,
          "Diet":"hf","Coat.Color":"black","GenerationLitter":"G4_2",
          "expression":0.3498,"_row":"F02"}
         ],
 "time":2.3
}

/mediate

Description: Perform mediation analysis.

Parameters:

Parameter Description
dataset dataset identifier
id the identifer to perform LOD scan on
mid marker identifier
expand TRUE to expand the JSON, FALSE to condense

Response: The response will be JSON.

Example Response:

{"result":[{"gene_id":"ENSMUSG00000000001","symbol":"Gnai3",
            "chr":"3","pos":108.1267,"LOD":1.3625},
           {"gene_id":"ENSMUSG00000000028","symbol":"Cdc45",
            "chr":"16","pos":18.7962,"LOD":1.605},
           ...
           {"gene_id":"ENSMUSG00000000037","symbol":"Scml2",
            "chr":"X","pos":161.1877,"LOD":1.2535}
     ],
 "time":10.3
}

/snpassoc

Description: SNP Association Mappting

Parameters:

Parameter Description
dataset dataset identifier
id the identifer to perform LOD scan on
chrom the chromosome
location chromosomal location
windowSize the window size, distance on each size of location
nCores number of cores to use
expand TRUE to expand the JSON, FALSE to condense

Response: The response will be JSON.

Example Response:

{"result":[{"snp":"rs245710663","chr":"1","pos":14.5001,
            "alleles":"G|C","sdp":64,"ensembl_gene":"",
            "csq":"intergenic_variant","index":1,"interval":147,
            "on_map":false,"lod":0.0015},
           {"snp":"rs263649601","chr":"1","pos":14.5002,
            "alleles":"C|T","sdp":64,"ensembl_gene":"",
            "csq":"intergenic_variant","index":1,"interval":147,
            "on_map":false,"lod":0.0015},
           ...
           {"snp":"rs32279922","chr":"1","pos":14.5004,
            "alleles":"C|T","sdp":153,"ensembl_gene":"",
            "csq":"intergenic_variant","index":3,"interval":147,
            "on_map":false,"lod":3.5395e-06}
         ],
 "time":11.1
}

/lodpeaks

Description: Peak LOD scors for a dataset.

Parameters:

Parameter Description
dataset dataset identifier
expand TRUE to expand the JSON, FALSE to condense

Response: The response will be JSON.

Example Response:

 {"result":[
     {"marker":"1_100007442","chr":"1","pos":100.0074,
      "gene_id":"ENSMUSG00000028028","symbol":"Alpk1",
      "gene_chrom":"3","middle":127.7255,"lod":6.1147
     },
     {"marker":"1_100078094","chr":"1","pos":100.0781,
      "gene_id":"ENSMUSG00000024727","symbol":"Trpm6",
      "gene_chrom":"19","middle":18.8212,"lod":6.048
     },
     ...
     {"marker":"1_100148722","chr":"1","pos":100.1487,
      "gene_id":"ENSMUSG00000045725","symbol":"Prr15",
      "gene_chrom":"6","middle":54.3286,"lod":6.5079
     }],
  "time":3.9
}

QTL Web

Overview

Docker and Docker Compose are the recommended way of running the QTL Web so it can be easily managed. A Docker image for the QTL API can be found on Docker Hub at mattjvincent/rqtlweb.

This image contains all the necessary code to run the QTL Web. An example docker-compose.yml can be found in the churchill-lab/qtlapi GitHub repository.

An example to start this Docker image is:

docker-compose up --scale api=3

For more in depth documentation, please refer to churchill-lab/qtlweb.

Tech Stack