get_mgi_features: Pull MGI gene tbl from SQLite database

In byandell/CCSanger: Utilities to get and use Sanger data for Collaborative Cross

Description

Get subset of MGI gene table from SQLite using chromosome interval. This is being replaced by query_variants. See package qtl2db.

Usage

get_mgi_features(chr_id, start_bp, end_bp, with_name = TRUE,
  gene_tbl = "mgi_gene", sql_file = "mgi_db.sqlite")

Arguments

chr_id	chromosome number
start_bp	starting position in bp
end_bp	ending position in bp
with_name	only pull named features if TRUE (default)
gene_tbl	character string of tbl to be used in database
sql_file	character string name of SQLite file (default "mgi_db.sqlite")

Value

tbl from SQLite database

Examples

dontrun(get_mgi_features(9, 104*1e6, 109*1e6))

byandell/CCSanger documentation built on May 13, 2019, 9:26 a.m.