create_gene_query_func: Create a function to query genes
In rqtl/qtl2db: Connect to Genome Databases for QTL Experiments

Description Usage Arguments Details Value Examples

View source: R/create_gene_query_func.R

Create a function that will connect to a SQLite database of gene information and return a data frame with gene information for a selected region.

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create_gene_query_func(dbfile = NULL, db = NULL, table_name = "genes",
  chr_field = "chr", start_field = "start", stop_field = "stop",
  filter = NULL)

`dbfile`	Name of database file
`db`	Optional database connection (provide one of `file` and `db`).
`table_name`	Name of table in the database
`chr_field`	Name of chromosome field
`start_field`	Name of field with start position (in basepairs)
`stop_field`	Name of field with stop position (in basepairs)
`filter`	Additional SQL filter (as a character string).

Note that this function assumes that the database has start and stop fields that are in basepairs, but the selection uses positions in Mbp, and the output data frame should have start and stop columns in Mbp.

Function with three arguments, chr, start, and end, which returns a data frame with the genes overlapping that region, with start and end being in Mbp. The output should contain at least the columns Name, chr, start, and stop, the latter two being positions in Mbp.

# create query function by connecting to file
dbfile <- system.file("extdata", "mouse_genes_small.sqlite", package="qtl2db")
query_genes <- create_gene_query_func(dbfile, filter="(source=='MGI')")
# query_genes will connect and disconnect each time
genes <- query_genes("2", 97.0, 98.0)

# connect and disconnect separately
library(RSQLite)
db <- dbConnect(SQLite(), dbfile)
query_genes <- create_gene_query_func(db=db, filter="(source=='MGI')")
genes <- query_genes("2", 97.0, 98.0)
dbDisconnect(db)