saveCNEToSQLite: Save CNE to SQLite

In ge11232002/CNEr: CNE Detection and Visualization

Save CNE to SQLite

Description

This function saves the CNE results into a local SQLite database.

Usage

  saveCNEToSQLite(x, dbName, tableName=NULL, overwrite=FALSE)

Arguments

x	An object of CNE, with CNEFinal computed or a GRangePairs object.
dbName	character(1): the filename of the local SQLite database.
tableName	character(1): the name of table for this CNE data table. When it is NULL, the table name will be inferred from the assembly filenames and scanning window/identity, in the format of "danRer10_hg38_49_50".
overwrite	boolean(1): whether or not to overwrite the existing table.

Details

before loading into an SQLite database, a bin indexing system is used to index the CNE range, which provides faster SQL query.

Author(s)

Ge Tan

Examples

  dbName <- tempfile()
  data(cneFinalListDanRer10Hg38)
  tableNames <- paste("danRer10", "hg38", names(cneFinalListDanRer10Hg38),
                      sep="_")
  for(i in 1:length(cneFinalListDanRer10Hg38)){
    saveCNEToSQLite(cneFinalListDanRer10Hg38[[i]], dbName, tableNames[i], 
                    overwrite=TRUE)
  }

ge11232002/CNEr documentation built on Oct. 26, 2022, 7:08 p.m.