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
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
|
\name{intra-range-methods}
\alias{intra-range-methods}
\alias{narrow}
\alias{narrow,GAlignments-method}
\alias{narrow,GAlignmentsList-method}
\alias{narrow,GappedReads-method}
\alias{qnarrow}
\alias{qnarrow,GAlignments-method}
\alias{qnarrow,GAlignmentsList-method}
\alias{qnarrow,GappedReads-method}
\title{Intra range transformations of a GAlignments or GAlignmentsList object}
\description{
This man page documents intra range transformations of a
\link{GAlignments} or \link{GAlignmentsList} object.
See \code{?`\link[IRanges]{intra-range-methods}`} and
\code{?`\link[IRanges]{inter-range-methods}`} in the \pkg{IRanges}
package for a quick introduction to intra range and inter range
transformations.
Intra range methods for \link{GRanges} and \link{GRangesList}
objects are defined and documented in the \pkg{GenomicRanges} package.
}
\usage{
\S4method{narrow}{GAlignments}(x, start=NA, end=NA, width=NA, use.names=TRUE)
\S4method{narrow}{GAlignmentsList}(x, start=NA, end=NA, width=NA, use.names=TRUE)
\S4method{qnarrow}{GAlignments}(x, start=NA, end=NA, width=NA)
\S4method{qnarrow}{GAlignmentsList}(x, start=NA, end=NA, width=NA)
}
\arguments{
\item{x}{
A \link{GAlignments} or \link{GAlignmentsList} object.
}
\item{start, end, width}{
Vectors of integers.
NAs and negative values are accepted and "solved" according to the
rules of the SEW (Start/End/Width) interface (see
\code{?\link[IRanges]{solveUserSEW}} for more information about the
SEW interface).
See \code{?`\link[IRanges]{intra-range-methods}`} for more information
about the \code{start}, \code{end}, and \code{width} arguments.
}
\item{use.names}{
See \code{?`\link[IRanges]{intra-range-methods}`}.
}
}
\details{
\itemize{
\item(){
\code{narrow} on a \link{GAlignments} object behaves
like on a \link[IRanges]{Ranges} object. See
\code{?`\link[IRanges]{intra-range-methods}`} for the details.
A major difference though is that it returns a \link{GAlignments}
object instead of a \link[IRanges]{Ranges} object.
Unlike with \code{qnarrow} (see below), the
\code{start}/\code{end}/\code{width} arguments here describe
the narrowing on the reference side, not the query side.
}
\item(){
\code{qnarrow} on a \link{GAlignments} object behaves like \code{narrow}
except that the \code{start}/\code{end}/\code{width} arguments here
specify the narrowing with respect to the query sequences.
\code{qnarrow} on a \link{GAlignmentsList} object
returns a \link{GAlignmentsList} object.
}
}
}
\value{
An object of the same class as, and \emph{parallel} to (i.e. same length
and names as), the original object \code{x}.
}
\note{
There is no difference between \code{narrow} and \code{qnarrow} when
all the alignments have a simple CIGAR (i.e. no indels or junctions).
}
\author{H. Pages and V. Obenchain <vobencha@fhcrc.org>}
\seealso{
\itemize{
\item \link{GAlignments} and \link{GAlignmentsList} objects.
\item The \link[IRanges]{intra-range-methods} man page in the
\pkg{IRanges} package.
\item The \link[GenomicRanges]{intra-range-methods} man page in the
\pkg{GenomicRanges} package.
}
}
\examples{
## ---------------------------------------------------------------------
## A. ON A GAlignments OBJECT
## ---------------------------------------------------------------------
ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
gal <- readGAlignments(ex1_file, param=ScanBamParam(what="flag"))
gal
## This trims 3 nucleotides on the left and 5 nucleotides on the right
## of each alignment:
qnarrow(gal, start=4, end=-6)
## Note that the 'start' and 'end' arguments specify what part of each
## query sequence should be kept (negative values being relative to the
## right end of the query sequence), not what part should be trimmed.
## Trimming on the left doesn't change the "end" of the queries.
qnarrow(gal, start=21)
stopifnot(identical(end(qnarrow(gal, start=21)), end(gal)))
## ---------------------------------------------------------------------
## B. ON A GAlignmentsList OBJECT
## ---------------------------------------------------------------------
gal1 <- GAlignments(
seqnames=Rle(factor(c("chr1", "chr2", "chr1", "chr3")),
c(1, 3, 2, 4)),
pos=1:10, cigar=paste0(10:1, "M"),
strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
names=head(letters, 10), score=1:10)
gal2 <- GAlignments(
seqnames=Rle(factor(c("chr2", "chr4")), c(3, 4)), pos=1:7,
cigar=c("5M", "3M2N3M2N3M", "5M", "10M", "5M1N4M", "8M2N1M", "5M"),
strand=Rle(strand(c("-", "+")), c(4, 3)),
names=tail(letters, 7), score=1:7)
galist <- GAlignmentsList(noGaps=gal1, Gaps=gal2)
galist
qnarrow(galist)
}
\keyword{methods}
\keyword{utilities}
|
