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\name{CNE-class}
\Rdversion{1.1}
\docType{class}
\alias{CNE}
\alias{CNE-class}
\alias{CNE12}
\alias{CNE12,CNE-method}
\alias{CNE21}
\alias{CNE21,CNE-method}
\alias{CNEMerged}
\alias{CNEMerged,CNE-method}
\alias{CNEFinal}
\alias{CNEFinal,CNE-method}
\alias{thresholds}
\alias{thresholds,CNE-method}
\title{Class \code{"CNE"}}
\description{
\code{CNE} class contains all the meta-data of CNEs, including the pair of
assemblies, the thresholds, the intermediate and final CNE sets.
}
\usage{
### Constructors:
CNE(assembly1Fn=character(1), assembly2Fn=character(1),
axt12Fn=character(), axt21Fn=character(),
window=50L, identity=50L,
CNE12=GRangePairs(), CNE21=GRangePairs(),
CNEMerged=GRangePairs(), CNEFinal=GRangePairs(),
aligner="blat", cutoffs1=4L, cutoffs2=4L)
### Accessor-like methods:
\S4method{thresholds}{CNE}(x)
\S4method{CNE12}{CNE}(x)
\S4method{CNE21}{CNE}(x)
\S4method{CNEMerged}{CNE}(x)
\S4method{CNEFinal}{CNE}(x)
## ... and more (see Methods)
}
\arguments{
\item{assembly1Fn,assembly2Fn}{Object of class \code{"character"}:
The twoBit filenames of assembly1, assembly2}
\item{axt12Fn,axt21Fn}{Object of class \code{"character"}:
The Axt filenames of assembly1 to assembly2, assembly2 to assembly1}
\item{window}{Object of class \code{"integer"}:
The window size for scanning CNEs. By default, it is 50.}
\item{identity}{Object of class \code{"integer"}:
The identity over the window size for scanning CNEs.
By default, it is 50.}
\item{CNE12}{Object of class \code{"GRangePairs"}:
The preliminary CNEs from axt file with assembly1 as reference.}
\item{CNE21}{Object of class \code{"GRangePairs"}:
The preliminary CNEs from axt file with assembly2 as reference.}
\item{CNEMerged}{Object of class \code{"GRangePairs"}:
The CNEs after merging CNE1 and CNE2.}
\item{CNEFinal}{Object of class \code{"GRangePairs"}:
The CNEs after being realigned back to reference genome,
with blat in current implementation.}
\item{aligner}{Object of class \code{"character"}:
The method to realign CNEs back to the reference genome.}
\item{cutoffs1, cutoffs2}{Object of class \code{"integer"}:
The CNEs with more than the cutoff hits on the reference genome
are removed.}
\item{x}{Object of class \code{"CNE"}:
A \code{"CNE"} object.}
}
\section{Methods}{
\describe{
\item{CNE12}{\code{signature(x = "CNE")}:
Get the CNE1 results.}
\item{CNE21}{\code{signature(x = "CNE")}:
Get the CNE2 results.}
\item{CNEMerged}{\code{signature(x = "CNE")}:
Get the merged CNE results.}
\item{CNEFinal}{\code{signature(x = "CNE")}:
Get the final CNE results.}
\item{thresholds}{\code{signature(x = "CNE")}:
Get the thresholds used for scanning CNEs.}
}
}
\author{
Ge Tan
}
\examples{
library(GenomicRanges)
## Constructor
CNE12 <- GRangePairs(first=GRanges(seqnames=c("chr13", "chr4", "chr4"),
ranges=IRanges(start=c(71727138,150679343,
146653164),
end=c(71727224, 150679400,
146653221)),
strand="+"),
second=GRanges(seqnames=c("chr1"),
ranges=IRanges(start=c(29854162, 23432387,
35711077),
end=c(29854248, 23432444,
35711134)),
strand="+")
)
CNE21 <- GRangePairs(first=GRanges(seqnames=c("chr1"),
ranges=IRanges(start=c(29854162, 23432387,
35711077),
end=c(29854248, 23432444,
35711134)),
strand="+"),
second=GRanges(seqnames=c("chr13", "chr4", "chr4"),
ranges=IRanges(start=c(71727138,150679343,
146653164),
end=c(71727224, 150679400,
146653221)),
strand="+")
)
cne <- CNE(assembly1Fn=file.path(system.file("extdata",
package="BSgenome.Drerio.UCSC.danRer10"),
"single_sequences.2bit"),
assembly2Fn=file.path(system.file("extdata",
package="BSgenome.Hsapiens.UCSC.hg38"),
"single_sequences.2bit"),
window=50L, identity=50L,
CNE12=CNE12, CNE21=CNE21, CNEMerged=CNE12, CNEFinal=CNE12,
aligner="blat", cutoffs1=4L, cutoffs2=4L)
## Accessor
CNE12(cne)
CNE21(cne)
thresholds(cne)
CNEMerged(cne)
CNEFinal(cne)
}
\keyword{classes}
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