readCNERangesFromSQLite: readCNERangesFromSQLite function

In CNEr: CNE Detection and Visualization

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)

CNEr documentation built on Nov. 8, 2020, 5:36 p.m.