Get integration sites from Database

For a given sample name gets integration site and matched random controls(MRCs).

Installation

From the R terminal or RStudio console run:

devtools::install_github("BushmanLab/intSiteRetriever")

If source is required, first get source from github(from bash):

git clone https://github.com/BushmanLab/intSiteRetriever.git

and from R terminal:

devtools::document()
devtools::install()
library(intSiteRetriever)

Connection to Database

For MySQL database config file should be in home directory and called .my.cnf.

.my.cnf file format is:

[GROUP_NAME]
user=YYYYYYY
password=XXXXXX
host=microbYYYY.med.upenn.edu
port=3309
database=intsites_miseq

We can establish connection in R:

dbConn <- dbConnect(MySQL(), group='GROUP_NAME')
info <- dbGetInfo(dbConn)
dbConn <- src_sql("mysql", dbConn, info = info)

The group should be the same as group in .my.cnf file. Note that by default connection will expire in about 5 minutes for MySQL.

#Interface

After connection is established we can get sites:

sample_ref <- data_frame(
    sampleName=c("sample1", "sample2"),
    refGenome=c("hg18", "hg18")
)
sites <- getUniqueSites(sample_ref, dbConn)

Public functions are:

• setNameExists
• getUniqueSites
• getUniqueSiteCounts
• getUniqueSiteReadCounts
• getUniquePCRbreaks
• getMultihitLengths
• getMRCs
• get_N_MRCs
• get_random_positions
• get_reference_genome

Documentation for functions:

?getUniqueSites

#Dependencies

Dependencies can be loaded with:

library(GenomicRanges)
library(BSgenome)
library(RMySQL)
library(dplyr)

Testing of the library components

Run in the R console:

library(devtools)
devtools::test()

Schema

Database schema is from file integration_site_schema.sql.

Continuous Integration

Travis is used for testing on each commit and Codecov used for code coverage metrics.