1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
|
\name{makeCNEDensity}
\alias{makeCNEDensity}
\title{
Make \sQuote{Bed}, \sQuote{bedGraph} and \sQuote{BigWig} files
}
\description{
Make \sQuote{Bed}, \sQuote{bedGraph}, \sQuote{BigWig} files
from \code{GRangePairs} for
display in other Genome Browser.
}
\usage{
makeCNEDensity(x, outputDir = ".",
genomeFirst = "first", genomeSecond = "second",
threshold = "50_50",
windowSizeFirst = 300L, windowSizeSecond = 300L)
}
\arguments{
\item{x}{
\code{GRangePairs} object of CNEs.
}
\item{outputDir}{
\code{character}(1): the output directory of
\sQuote{Bed}, \sQuote{bedGraph} and \sQuote{BigWig} files.
}
\item{genomeFirst,genomeSecond}{
\code{character}(1): the genome name of the first and second species.
}
\item{threshold}{
\code{character}(1): the threshold used to identify the CNEs
in format of "50_50".
}
\item{windowSizeFirst,windowSizeSecond}{
\code{integer}(1): the smoothing window size for generating the CNE density
in kb.
}
}
\details{
The CNE density is defined as the percentage of regions covered by CNEs
within the smoothing window.
}
\value{
The filenames of output \sQuote{Bed}, \sQuote{bedGraph} and
\sQuote{BigWig} files.
}
\author{
Ge Tan
}
\note{
This function is mainly for internal use in Lenhard group.
}
\seealso{
\code{\link{readAncora}}
}
\examples{
\dontrun{
dbName <- file.path(system.file("extdata", package="CNEr"),
"danRer10CNE.sqlite")
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")
cneGRangePairs <- readCNERangesFromSQLite(dbName=dbName,
tableName="danRer10_hg38_45_50",
tAssemblyFn=tAssemblyFn,
qAssemblyFn=qAssemblyFn)
makeCNEDensity(cneGRangePairs[1:1000])
}
}
|
