CNEDensity: CNEDensity function

In CNEr: CNE Detection and Visualization

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)

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