readCNERangesFromSQLite {CNEr} | R Documentation

## readCNERangesFromSQLite function

### Description

Query the SQLite database based on chromosome, coordinates and some other criteria. Primarily not intended to be used directly. For the CNE density plot, `fetchCNEDensity` function should be used.

### Usage

    readCNERangesFromSQLite(dbName, tableName, chr=NULL, start=NULL, end=NULL,
                            whichAssembly=c("first","second"), minLength=NULL,
                            tAssemblyFn=NULL, qAssemblyFn=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` | `character`(n): the chromosomes to query. When it's NULL, all CNEs will be returned.
`start, end` | `integer`(n): the start and end coordinates to fetch the CNEs.
`whichAssembly` | `character`(1): The coordinates to fetch CNEs are based on ‘first’ genome or ‘last’ genome.
`minLength` | `integer`(1): the minimal length for selected CNEs. The pair of CNEs must be both longer than this `minLength`.
`tAssemblyFn,qAssemblyFn` | `character`(1): filename of the ‘twoBit’ or ‘fasta’ file for the target and query genome.

### Value

An object of `GRangePairs` is returned.

### Author(s)

Ge Tan

### Examples

      dbName <- file.path(system.file("extdata", package="CNEr"),
                        "danRer10CNE.sqlite")
      tableName <- "danRer10_hg38_45_50"

      qAssemblyFn <- file.path(system.file("extdata",
                               package="BSgenome.Hsapiens.UCSC.hg38"),
                               "single_sequences.2bit")
      tAssemblyFn <- file.path(system.file("extdata",
                               package="BSgenome.Drerio.UCSC.danRer10"),
                               "single_sequences.2bit")

      ## single chr, start, end
      chr <- "chr6"
      start <- 24000000L
      end <-  27000000
      minLength <- 50L
      fetchedCNERanges <- readCNERangesFromSQLite(dbName, tableName, chr,
                                                  start, end,
                                                  whichAssembly="first",
                                                  minLength=minLength,
                                                  tAssemblyFn=tAssemblyFn,
                                                  qAssemblyFn=qAssemblyFn)
      ## multiple chr, start, end
      chr=c("chr1", "chr3")
      start=c(90730248, 137523122)
      end=c(90730300, 137523190)
      fetchedCNERanges <- readCNERangesFromSQLite(dbName, tableName, chr,
                                                  start, end,
                                                  whichAssembly="second",
                                                  minLength=minLength)

      ## chr, NULL, NULL
      fetchedCNERanges <- readCNERangesFromSQLite(dbName, tableName, chr,
                                                  start=NULL, end=NULL,
                                                  whichAssembly="second",
                                                  minLength=minLength)

[Package CNEr version 1.20.0 Index]