CNEr (version 1.8.3)

CNEDensity-methods: CNEDensity function

Description

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

Usage

CNEDensity(dbName, tableName, assembly1, assembly2, threshold, chr, start, end, windowSize, 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. It can be missing when assembly1, assembly2 and threshold are provided.

assembly1

A object of character, the assembly to search.

assembly2

The comparison assembly. It can be missing when tableName is provided.

threshold

The threshold to search. It can be missing when tableName is provided.

chr

A object of character, the chromosome to query.

start, end

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

windowSize

A object of integer, the window size in kb used to smooth the CNEs.

minLength

A object of integer, the minimal length of CNEs to fetch.

Value

A matrix is returned. The first column is the coordinates and the second column is the density values.

Methods

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

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

Examples

    dbName <- file.path(system.file("extdata", package="CNEr"),
                        "cne.sqlite")
    chr <- "chr11"
    start <- 31000000L
    end <-  33000000L
    windowSize <- 300L
    minLength <- 50L
    cneHg19DanRer7_45_50 <- 
      CNEDensity(dbName=dbName, 
                 tableName="danRer7_hg19_45_50", 
                 assembly1="hg19", chr=chr, start=start,
                 end=end, windowSize=windowSize, 
                 minLength=minLength)
    cneHg19DanRer7_48_50 <- 
      CNEDensity(dbName=dbName, 
                 tableName="danRer7_hg19_45_50", 
                 assembly1="hg19", chr=chr, start=start,
                 end=end, windowSize=windowSize, 
                 minLength=minLength)
    cneHg19DanRer7_49_50 <- 
      CNEDensity(dbName=dbName, 
                 tableName="danRer7_hg19_45_50", 
                 assembly1="hg19", chr=chr, start=start,
                 end=end, windowSize=windowSize, 
                 minLength=minLength)