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\name{CNEDensity-methods}
\docType{methods}
\alias{CNEDensity}
\alias{CNEDensity-methods}
\alias{CNEDensity,ANY,character,character,missing,missing-method}
\alias{CNEDensity,ANY,missing,character,character,character-method}
\title{
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{
\item{dbName}{
\code{character}(1): the path of the local SQLite database.
}
\item{tableName}{
\code{character}(1): the name of table for this CNE data table.
It can be missing when assembly1, assembly2 and threshold are provided.
}
\item{chr}{
\code{character}(1): the chromosome to query.
}
\item{start, end}{
\code{integer}(1): the start and end coordinate to fetch the CNEs.
}
\item{whichAssembly}{
\code{character}(1):
the genome to fetch is in the \sQuote{first} column or \sQuote{second}
column of the table.
}
\item{windowSize}{
\code{integer}(1): the window size in kb that is used to smooth the CNEs.
}
\item{minLength}{
\code{integer}(1): the minimal length of CNEs to fetch.
}
}
\section{Methods}{
\describe{
\item{\code{signature(tableName = "character",
assembly1 = "character", assembly2 = "missing",
threshold = "missing")}}{
}
\item{\code{signature(tableName = "missing", assembly1 = "character",
assembly2 = "character", threshold = "character")}}{
}
}}
\value{
A \code{GRanges} object with density values is returned.
}
\author{
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)
}
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