This is an API which is used to pull down results from the GoDMC meta analysis of genetic influences on DNA methylation levels.

Most methods are using get - you put in a specific query and the result is returned.

There are also more complex queries that can be obtained using post. Here a json file needs to be built that describes the query.

All results are json format. At the bottom of this page we describe how you can use R to access the API.

Get a list of all cohorts

/v0.1/cohorts

e.g. http://api.godmc.org.uk/v0.1/cohorts

Get mQTLs for a specific SNP or CpG

/v0.1/assoc_meta/cpg/<cpgid>
/v0.1/assoc_meta/rsid/<rsid>
/v0.1/assoc_meta/snp/<snpid>

e.g. http://api.godmc.org.uk/v0.1/assoc_meta/cpg/cg17242362

e.g. http://api.godmc.org.uk/v0.1/assoc_meta/rsid/rs6602381

e.g. http://api.godmc.org.uk/v0.1/assoc_meta/snp/chr10:10000018:SNP

The -log10(p-values) for all associations with a particular SNP or CpG can be obtained in bed or BigBed format as:

/v0.1/dl/<format>/cpg/<cpgid>
/v0.1/dl/<format>/snp/<snpid>

e.g. http://api.godmc.org.uk/v0.1/dl/bigbed/cpg/cg17242362

e.g. http://api.godmc.org.uk/v0.1/dl/bed/snp/chr10:10000018:SNP

Get all mQTLs where a SNP or CpG is within some range

/v0.1/assoc_meta/range/<attribute>/<chrrange>

Note: this is a bit slow due to database, needs to be improved

e.g. http://api.godmc.org.uk/v0.1/assoc_meta/range/cpg/10:10000000-10100000

e.g. http://api.godmc.org.uk/v0.1/assoc_meta/range/snp/10:10000000-10100000

Get all mQTLs where a SNP or CpG is within 25kb of a gene start site

/v0.1/assoc_meta/gene/<attribute>/<gene>

Note: this is a bit slow due to database, needs to be improved

e.g. http://api.godmc.org.uk/v0.1/assoc_meta/gene/cpg/A1BG

e.g. http://api.godmc.org.uk/v0.1/assoc_meta/gene/snp/A1BG

Get a list of all genes

/v0.1/list/gene

e.g. http://api.godmc.org.uk/v0.1/list/gene

Get information about a SNP, CpG or gene

/v0.1/info/<attribute>/<item>

e.g. http://api.godmc.org.uk/v0.1/info/cpg/cg26866020

e.g. http://api.godmc.org.uk/v0.1/info/gene/A1BG

e.g. http://api.godmc.org.uk/v0.1/info/rsid/rs234

e.g. http://api.godmc.org.uk/v0.1/info/snp/chr7:105561135:SNP

More complex queries

There is a limit to the length of a URL, so if you want to extract a large list of SNPs then we need to post the query details through a file. This can be done through curl e.g. using:

curl -i -H "Content-Type: application/json" -X POST -d @test.json http://api.godmc.org.uk/v0.1/query

Here we are posting the test.json file that contains the details of the query. Examples below

Query multiple SNPs, test.json:

{
    "snps": ["chr10:100003302:SNP", "chr10:99954538:INDEL", "chr10:99981275:SNP"]
}

Query multiple rsids, test.json:

{
    "rsids": ["rs6602381", "rs72828459", "rs234"]
}

Query multiple CpGs, test.json:

{
    "cpgs": ["cg14380065", "cg12715136"]
}

Query mQTLs for rsids and CpGs, (i.e. get all results where an mQTL contains a SNP and a CpG specified in the lists), test.json:

{
    "rsids": ["rs6602381", "rs72828459", "rs234"],
    "cpgs": ["cg14380065", "cg12715136"]
}

As in the third example but set p-value threshold, only return cis effects, return only clumped rows, and specify which columns to return, test.json:

{
    "cpgs": ["cg02518338", "cg12715136"],
    "pval": 1e-10,
    "cistrans": "cis",
    "clumped": 1,
    "columns": "pval, cpg, cistrans, clumped"
}

Note that if the clumped and cistrans fields are not set then no filtering is done. If clumped = 0 then only the unclumped results are returned. If cistrans = "" then both cis and trans results are returned. Similarly, if the pval field is not set then no filter is applied.

Using R

You can access the data through GET methods, as demonstrated in the following example:

if(!require(jsonlite)){
    install.packages("jsonlite")
}
library(jsonlite)
mqtl_data <- fromJSON("http://api.godmc.org.uk/v0.1/assoc_meta/cpg/cg17242362")

i.e. you are just getting JSON downloads from the URL. You can also run more complex queries following the POST format:

if(!require(httr)){
    install.packages("httr")
}
if(!require(dplyr)){
    install.packages("dplyr")
}
library(httr)
library(dplyr)
query <- list(
    cpgs = c("cg02518338", "cg12715136"),
    pval = 1e-10,
    clumped = 1
)
res <- POST("http://api.godmc.org.uk/v0.1/query", body = query, encode = "json")
content(res) %>% lapply(., as_data_frame) %>% bind_rows