src_biogridr: Connect to local BioGRID database

In EricEdwardBryant/biogridr: BioGRID Interaction Data

Description

Connect to the biogridr package's interaction database

Usage

src_biogridr(path = getOption("biogridr.db"))

Arguments

path	Path to BioGRID SQLite database. Defaults to getOption('biogridr.db').

Details

BioGRID interactions are stored in a local SQLite database, and src_biogridr() returns a connection to this database via dplyr. This allows the user to aviod loading all 700,000+ interactions into memory by using dplyr to select columns and filter rows.

Examples

## Not run: 

# First download all interaction data
# WARNING: This takes a few minutes!
update_biogridr()

# Connect to the database
db <- src_biogridr()

# Query the database for a CTF4 outer network 
outer_net(db, 'CTF4')

# Aggregate the CTF4 outer network
aggregate(outer_net('CTF4'))

# Use dplyr to make custom queries to the database
library(dplyr)
tbl(db, 'systems')
tbl(db, 'organisms')

genes <- c('TOF1', 'CTF4')
organism <- organism('cerevisiae')
tbl(db, 'interactions') %>%
  filter(
    (a %in% genes | b %in% genes) &
     a_organism == organism &
     b_organism == organism
  ) %>%
  select(a, b) %>%
  collect()

## End(Not run)

EricEdwardBryant/biogridr documentation built on May 6, 2019, 4:02 p.m.