CNEr (version 1.8.3)

readCNERangesFromSQLite: readCNERangesFromSQLite function

Description

Query the SQLite database based on chromosome, coordiantes and some other criterias. Usually not to be used directly. For the CNE density plot, fetchCNEDensity function should be used.

Usage

readCNERangesFromSQLite(dbName, tableName, chr, start, end, whichAssembly=c("L","R"), minLength=NULL)

Arguments

dbName

A object of character, the path of the local SQLite database.

tableName

A object of character, the name of table for this CNE data table.

chr

A object of character, the chromosome to query

start, end

A object of integer, the start and end coordiante to fetch the CNEs.

whichAssembly

A object of character, the genome to fetch is in the "Left" columns or "Right" columns of the table.

minLength

A object of integer, the minimal length for selected CNEs.

Value

A object of IRanges is retu

Examples

    dbName <- file.path(system.file("extdata", package="CNEr"),
                       "cne.sqlite")
    chr <- "chr11"
    start <- 31000000L
    end <-  33000000L
    minLength <- 50L
    tableName <- "danRer7_hg19_45_50"
    fetchedCNERanges <- readCNERangesFromSQLite(dbName, tableName, chr, 
                                               start, end, whichAssembly="L",
                                               minLength=minLength)