inst/scripts/ReadMe.md

In rqtl/qtl2db: Connect to Genome Databases for QTL Experiments

qtl2db scripts

This directory contains four R scripts, for creating SQLite databases for use with the Collaborative Cross (CC) and Diversity Outbred (DO) mouse populations:

• create_ccvariants.R creates the database cc_variants.sqlite which combines data on SNPs, indels, and structural variants in the eight CC founders.

• create_mousegenes.R creates the database mouse_genes.sqlite which mouse gene locations from the Mouse Genome Informatics (MGI) database. Key fields in the resulting database include

• source (e.g., "MGI")

• type
• start (in basepairs)
• stop (in basepairs)
• strand

• Name

• create_ccvariants_small.R creates ../extdata/cc_variants_small.sqlite, a small version of cc_variants.sqlite for use in tests. This contains the variants within two small regions (one on chr 2 and one on chr 3).

• create_mousegenes_small.R creates ../extdata/mouse_genes_small.sqlite, a small version of mouse_genes.sqlite for use in tests. This contains the genes with source=="MGI" that overlap two small regions (one on chr 2 and one on chr 3).

• create_mousegenes_mgi.R creates mouse_genes_mgi.sqlite, a version with just the records with source=="MGI".

Using these scripts to constructing these databases requires the following R packages:

• data.table
• RSQLite
• VariantAnnotation
• R/qtl2scan

The larger database files created by these scripts are available for direct download from figshare:

• cc_variants.sqlite doi:10.6084/m9.figshare.5280229.v1
• mouse_genes.sqlite doi:10.6084/m9.figshare.5280238.v3

A smaller version of the mouse genes database, with just the records with source=="MGI", is also available at figshare:

• mouse_genes_mgi.sqlite doi:10.6084/m9.figshare.5286019.v4

rqtl/qtl2db documentation built on May 18, 2019, 9:18 p.m.