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
|
\name{GappedReads-class}
\docType{class}
% Class:
\alias{GappedReads-class}
\alias{GappedReads}
% Accessors:
\alias{qseq}
\alias{qseq,GappedReads-method}
\alias{qwidth,GappedReads-method}
% Combining:
\alias{c,GappedReads-method}
\title{(Legacy) GappedReads objects}
\description{
The GappedReads class extends the \link{GAlignments} class.
A GappedReads object contains all the information contained in a
\link{GAlignments} object plus the sequences of the queries.
Those sequences can be accessed via the \code{qseq} accessor.
}
\section{Constructor}{
GappedReads objects are typically created when reading a file
containing aligned reads with the \code{\link{readGappedReads}}
function.
}
\section{Accessors}{
In the code snippets below, \code{x} is a GappedReads object.
\describe{
\item{}{
\code{qseq(x)}:
Extracts the sequences of the queries as a
\code{\link[Biostrings]{DNAStringSet}} object.
}
}
}
\references{
\url{http://samtools.sourceforge.net/}
}
\author{
H. Pages and P. Aboyoun
}
\seealso{
\itemize{
\item \link{GAlignments} objects.
\item \code{\link{readGappedReads}}.
}
}
\examples{
greads_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
greads <- readGappedReads(greads_file)
greads
qseq(greads)
}
\keyword{methods}
\keyword{classes}
|
