README.md

In andrewparkermorgan/genodb: R Access to Genotype Databases

genodb

An R package for interacting with UNC Systems Genetics genotype databases for the MUGA family of arrays.

Dependencies

For R:

• DBI, RSQLite -- generic databse machinery
• data.table -- efficient representation of in-memory tables

For python:

• python (>= 2.7)
• sqlite3

Usage

library(genodb)

options(genodb.MMDBPATH = "/path/to/my/database")

load("~/db/arrays/megamuga/snps.megamuga.Rdata")
ss <- fetch.samples("DBA/2%", exact = FALSE)
geno <- make.genotypes(ss$id, snps, by = "id", chr = "M")

summary(geno)

andrewparkermorgan/genodb documentation built on May 10, 2019, 11:09 a.m.