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\name{readCNERangesFromSQLite}
\alias{readCNERangesFromSQLite}
\title{
readCNERangesFromSQLite function
}
\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, \code{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{
\item{dbName}{
A object of \code{character}, the path of the local SQLite database.
}
\item{tableName}{
A object of \code{character}, the name of table for this CNE data table.
}
\item{chr}{
\code{character}(n): the chromosomes to query.
When it's NULL, all CNEs will be returned.
}
\item{start, end}{
\code{integer}(n): the start and end coordinates to fetch the CNEs.
}
\item{whichAssembly}{
\code{character}(1):
The coordinates to fetch CNEs are based on \sQuote{first} genome or
\sQuote{last} genome.
}
\item{minLength}{
\code{integer}(1): the minimal length for selected CNEs.
The pair of CNEs must be both longer than this \code{minLength}.
}
\item{tAssemblyFn,qAssemblyFn}{
\code{character}(1): filename of the \sQuote{twoBit} or \sQuote{fasta}
file for the target and query genome.
}
}
\value{
An object of \code{GRangePairs} is returned.
}
\author{
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)
}
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