CNEDensity-methods {CNEr} | R Documentation

## CNEDensity function

### Description

This function queries the database and generates the CNEs' density values.

### Usage

    CNEDensity(dbName, tableName, chr, start, end,
               whichAssembly=c("first", "second"),
               windowSize=300, minLength=NULL)

### Arguments

`dbName` | `character`(1): the path of the local SQLite database.
`tableName` | `character`(1): the name of table for this CNE data table. It can be missing when assembly1, assembly2 and threshold are provided.
`chr` | `character`(1): the chromosome to query.
`start, end` | `integer`(1): the start and end coordinate to fetch the CNEs.
`whichAssembly` | `character`(1): the genome to fetch is in the ‘first’ column or ‘second’ column of the table.
`windowSize` | `integer`(1): the window size in kb that is used to smooth the CNEs.
`minLength` | `integer`(1): the minimal length of CNEs to fetch.

### Value

A `GRanges` object with density values is returned.

### Methods

`signature(tableName = "character", assembly1 = "character", assembly2 = "missing", threshold = "missing")`
`signature(tableName = "missing", assembly1 = "character", assembly2 = "character", threshold = "character")`

### Author(s)

Ge Tan

### Examples

    dbName <- file.path(system.file("extdata", package="CNEr"),
                        "danRer10CNE.sqlite")
    genome <- "danRer10"
    chr <- "chr6"
    start <- 24000000L
    end <-  27000000L
    windowSize <- 200L
    minLength <- 50L
    cneDanRer10Hg38_45_50 <-
      CNEDensity(dbName=dbName,
                 tableName="danRer10_hg38_45_50",
                 whichAssembly="first", chr=chr, start=start,
                 end=end, windowSize=windowSize,
                 minLength=minLength)
    cneDanRer10Hg38_49_50 <-
      CNEDensity(dbName=dbName,
                 tableName="danRer10_hg38_49_50",
                 whichAssembly="first", chr=chr, start=start,
                 end=end, windowSize=windowSize,
                 minLength=minLength)

[Package CNEr version 1.20.0 Index]