In shwetagopaul92/txregquery: Query txregnet data

MongoDB Atlas

Delivers the world’s leading database for modern applications as a fully automated cloud service.
Proven operational and security practices are built in, automating time-consuming administration tasks such as infrastructure provisioning, database setup, ensuring availability, global distribution, backups, and more.
The easy-to-use UI and API let you spend more time building your applications and less time managing your database.

Available Plans

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How to work with MongoDB Atlas

Create an Atlas User Account
Create an Atlas Free Tier Cluster

Connect to a Cluster

Check the IP Whitelist
Choose a Connection Method ( mongo shell )
Start a terminal and enter the connection command, enter password when prompted
Can perform mongo commands from here

Import data into a Cluster

Grab the cluster name for --host

mongoimport --host cluster0-shard-00-00-ag7nd.mongodb.net:27017 --db encode --type csv --file cebpbgr.csv --authenticationDatabase admin --ssl --username reshg --password

Datasets on MongoDb Atlas

Database Name : txregnet DATABASE SIZE : 4.42GB INDEX SIZE : 400.1MB TOTAL COLLECTIONS : 45

Query the data from R

To query the 10 CEBPB GRanges collection

library(mongolite)
url="mongodb+srv://def:def@cluster1-ag7nd.mongodb.net/test"
mongo(collection="cebpbgr",db="encode",url=url)

Query data using TxRegQuery

To query eqtl data

library(TxRegQuery)
mychrGo=17
mystartGo=41196312-500*1000
myendGo=41322262+500*1000
mycollGo="Whole_Blood_allpairs_v7_eQTL"
mydbGo="txregnet"
url="mongodb+srv://def:def@cluster1-ag7nd.mongodb.net/test"
res_eqtl=getAtlasRangeEqtl(mychrGo,mystartGo,myendGo,mycollGo,mydbGo,url)
res_eqtl