This directory contains five 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:
The larger database files created by these scripts are available for direct download from figshare:
cc_variants.sqlite
doi:10.6084/m9.figshare.5280229.v3mouse_genes.sqlite
doi:10.6084/m9.figshare.5280238.v7A smaller version of the mouse genes database, with just the records
with source=="MGI"
, is also available at
figshare:
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