1. SummarizedExperiment
  2. man
  3. intra-range-methods.Rd
Browse code

Add terminators() method, same as promoters() but for terminator regions

Hervé Pagès authored on 22/01/2024 23:49:52
Showing 1 changed files
man/intra-range-methods.Rd
History View file @ 6b32ed4
... ... 
@@ -15,7 +15,9 @@
15 15 
 \alias{flank,RangedSummarizedExperiment-method}
16 16
17 17 
 \alias{promoters}
18 
+\alias{terminators}
18 19 
 \alias{promoters,RangedSummarizedExperiment-method}
20 
+\alias{terminators,RangedSummarizedExperiment-method}
19 21
20 22 
 \alias{restrict}
21 23 
 \alias{restrict,RangedSummarizedExperiment-method}
... ... 
@@ -42,6 +44,7 @@
42 44 
       use.names=TRUE, ignore.strand=FALSE)
43 45
44 46 
 \S4method{promoters}{RangedSummarizedExperiment}(x, upstream=2000, downstream=200)
47 
+\S4method{terminators}{RangedSummarizedExperiment}(x, upstream=2000, downstream=200)
45 48
46 49 
 \S4method{restrict}{RangedSummarizedExperiment}(x, start=NA, end=NA, keep.all.ranges=FALSE,
47 50 
          use.names=TRUE)
... ... 
@@ -53,21 +56,10 @@
53 56 
   \item{x}{
54 57 
     A \link{RangedSummarizedExperiment} object.
55 58 
   }
56 
-  \item{shift, use.names}{
57 
-    See \code{?\link{shift}} in the \pkg{IRanges}
58 
-    package.
59 
-  }
60 
-  \item{start, end, width, fix}{
61 
-    See \code{?\link{shift}} in the \pkg{IRanges} package.
62 
-  }
63 
-  \item{ignore.strand, both}{
64 
-    See \code{?\link{shift}} in the \pkg{IRanges} package.
65 
-  }
66 
-  \item{upstream, downstream}{
67 
-    See \code{?\link{shift}} in the \pkg{IRanges} package.
68 
-  }
69 
-  \item{keep.all.ranges}{
70 
-    See \code{?\link{shift}} in the \pkg{IRanges} package.
59 
+  \item{shift, use.names, start, end, width, fix, ignore.strand, both,
60 
+        upstream, downstream, keep.all.ranges}{
61 
+    See \code{?GenomicRanges::\link[GenomicRanges]{shift}} in the
62 
+    \pkg{GenomicRanges} package.
71 63 
   }
72 64 
 }
73 65
... ... 
@@ -84,9 +76,10 @@
84 76 
   where \code{f} is the name of the function and \code{...} any additional
85 77 
   arguments passed to it.
86 78
87 
-  See \code{?\link{shift}} in the \pkg{IRanges}
88 
-  package for the details of how these transformations operate on a
89 
-  \link[GenomicRanges]{GenomicRanges} or \link[GenomicRanges]{GRangesList}
79 
+  See \code{?GenomicRanges::\link[GenomicRanges]{shift}} in the
80 
+  \pkg{GenomicRanges} package for the details of how these transformations
81 
+  operate on a \link[GenomicRanges]{GenomicRanges} or
82 
+  \link[GenomicRanges]{GRangesList}
90 83 
   object.
91 84 
 }
92 85
... ... 
@@ -94,8 +87,8 @@
94 87 
   \itemize{
95 88 
     \item \link{RangedSummarizedExperiment} objects.
96 89
97 
-    \item The \link{shift} man page in the
98 
-          \pkg{IRanges} package where \emph{intra range transformations}
90 
+    \item The \code{\link[GenomicRanges]{shift}} man page in the
91 
+          \pkg{GenomicRanges} package where \emph{intra range transformations}
99 92 
           of a \link[GenomicRanges]{GenomicRanges} or
100 93 
           \link[GenomicRanges]{GRangesList} object are documented.
101 94 
   }
... ... 
@@ -136,9 +129,21 @@ stopifnot(identical(
136 129 
   flank(rowRanges(rse0), width=20)
137 130 
 ))
138 131
139 
-se5 <- restrict(rse0, start=200, end=700, keep.all.ranges=TRUE)
132 
+se5 <- promoters(rse0, upstream=85, downstream=50)
140 133 
 stopifnot(identical(
141 134 
   rowRanges(se5),
135 
+  promoters(rowRanges(rse0), upstream=85, downstream=50)
136 
+))
137 
+
138 
+se6 <- terminators(rse0, upstream=85, downstream=50)
139 
+stopifnot(identical(
140 
+  rowRanges(se6),
141 
+  terminators(rowRanges(rse0), upstream=85, downstream=50)
142 
+))
143 
+
144 
+se7 <- restrict(rse0, start=200, end=700, keep.all.ranges=TRUE)
145 
+stopifnot(identical(
146 
+  rowRanges(se7),
142 147 
   restrict(rowRanges(rse0), start=200, end=700, keep.all.ranges=TRUE)
143 148 
 ))
144 149 
 }
Browse code

shift() documentation is not in GenomicRanges:shift

Martin Morgan authored on 04/06/2018 15:33:37
Showing 1 changed files
man/intra-range-methods.Rd
History View file @ 1e2aedf
... ... 
@@ -54,24 +54,20 @@
54 54 
     A \link{RangedSummarizedExperiment} object.
55 55 
   }
56 56 
   \item{shift, use.names}{
57 
-    See \code{?\link[GenomicRanges]{shift}} in the \pkg{GenomicRanges}
57 
+    See \code{?\link{shift}} in the \pkg{IRanges}
58 58 
     package.
59 59 
   }
60 60 
   \item{start, end, width, fix}{
61 
-    See \code{?\link[GenomicRanges]{shift}} in the \pkg{GenomicRanges}
62 
-    package.
61 
+    See \code{?\link{shift}} in the \pkg{IRanges} package.
63 62 
   }
64 63 
   \item{ignore.strand, both}{
65 
-    See \code{?\link[GenomicRanges]{shift}} in the \pkg{GenomicRanges}
66 
-    package.
64 
+    See \code{?\link{shift}} in the \pkg{IRanges} package.
67 65 
   }
68 66 
   \item{upstream, downstream}{
69 
-    See \code{?\link[GenomicRanges]{shift}} in the \pkg{GenomicRanges}
70 
-    package.
67 
+    See \code{?\link{shift}} in the \pkg{IRanges} package.
71 68 
   }
72 69 
   \item{keep.all.ranges}{
73 
-    See \code{?\link[GenomicRanges]{shift}} in the \pkg{GenomicRanges}
74 
-    package.
70 
+    See \code{?\link{shift}} in the \pkg{IRanges} package.
75 71 
   }
76 72 
 }
77 73
... ... 
@@ -88,7 +84,7 @@
88 84 
   where \code{f} is the name of the function and \code{...} any additional
89 85 
   arguments passed to it.
90 86
91 
-  See \code{?\link[GenomicRanges]{shift}} in the \pkg{GenomicRanges}
87 
+  See \code{?\link{shift}} in the \pkg{IRanges}
92 88 
   package for the details of how these transformations operate on a
93 89 
   \link[GenomicRanges]{GenomicRanges} or \link[GenomicRanges]{GRangesList}
94 90 
   object.
... ... 
@@ -98,8 +94,8 @@
98 94 
   \itemize{
99 95 
     \item \link{RangedSummarizedExperiment} objects.
100 96
101 
-    \item The \link[GenomicRanges]{shift} man page in the
102 
-          \pkg{GenomicRanges} package where \emph{intra range transformations}
97 
+    \item The \link{shift} man page in the
98 
+          \pkg{IRanges} package where \emph{intra range transformations}
103 99 
           of a \link[GenomicRanges]{GenomicRanges} or
104 100 
           \link[GenomicRanges]{GRangesList} object are documented.
105 101 
   }
Browse code

Add 'rowData' argument to SummarizedExperiment() constructor. This allows the user to supply the row data at construction time.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SummarizedExperiment@111282 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 07/12/2015 23:48:18
Showing 1 changed files
man/intra-range-methods.Rd
History View file @ 3758905
... ... 
@@ -113,37 +113,37 @@ rowRanges <- GRanges(rep(c("chr1", "chr2"), c(5, 15)),
113 113 
                      strand=Rle(c("+", "-"), c(12, 8)))
114 114 
 colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
115 115 
                      row.names=LETTERS[1:6])
116 
-se0 <- SummarizedExperiment(assays=SimpleList(counts=counts),
117 
-                            rowRanges=rowRanges, colData=colData)
116 
+rse0 <- SummarizedExperiment(assays=SimpleList(counts=counts),
117 
+                             rowRanges=rowRanges, colData=colData)
118 118
119 
-se1 <- shift(se0, 1)
119 
+rse1 <- shift(rse0, 1)
120 120 
 stopifnot(identical(
121 
-  rowRanges(se1),
122 
-  shift(rowRanges(se0), 1)
121 
+  rowRanges(rse1),
122 
+  shift(rowRanges(rse0), 1)
123 123 
 ))
124 124
125 
-se2 <- narrow(se0, start=10, end=-15)
125 
+se2 <- narrow(rse0, start=10, end=-15)
126 126 
 stopifnot(identical(
127 127 
   rowRanges(se2),
128 
-  narrow(rowRanges(se0), start=10, end=-15)
128 
+  narrow(rowRanges(rse0), start=10, end=-15)
129 129 
 ))
130 130
131 
-se3 <- resize(se0, width=75)
131 
+se3 <- resize(rse0, width=75)
132 132 
 stopifnot(identical(
133 133 
   rowRanges(se3),
134 
-  resize(rowRanges(se0), width=75)
134 
+  resize(rowRanges(rse0), width=75)
135 135 
 ))
136 136
137 
-se4 <- flank(se0, width=20)
137 
+se4 <- flank(rse0, width=20)
138 138 
 stopifnot(identical(
139 139 
   rowRanges(se4),
140 
-  flank(rowRanges(se0), width=20)
140 
+  flank(rowRanges(rse0), width=20)
141 141 
 ))
142 142
143 
-se5 <- restrict(se0, start=200, end=700, keep.all.ranges=TRUE)
143 
+se5 <- restrict(rse0, start=200, end=700, keep.all.ranges=TRUE)
144 144 
 stopifnot(identical(
145 145 
   rowRanges(se5),
146 
-  restrict(rowRanges(se0), start=200, end=700, keep.all.ranges=TRUE)
146 
+  restrict(rowRanges(rse0), start=200, end=700, keep.all.ranges=TRUE)
147 147 
 ))
148 148 
 }
149 149
Browse code

some minor edits

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SummarizedExperiment@103860 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 15/05/2015 08:11:29
Showing 1 changed files
man/intra-range-methods.Rd
History View file @ dd19136
... ... 
@@ -26,16 +26,8 @@
26 26 
 \title{Intra range transformations of a RangedSummarizedExperiment object}
27 27
28 28 
 \description{
29 
-  This man page documents \emph{intra range transformations} of a
30 
-  \link{RangedSummarizedExperiment} object. These transformations
31 
-  operate on the \code{rowRanges} component of the object, which can be a
32 
-  \link[GenomicRanges]{GenomicRanges} or \link[GenomicRanges]{GRangesList}
33 
-  object.
34 
-
35 
-  See \code{?\link[GenomicRanges]{shift}} in the \pkg{GenomicRanges}
36 
-  package for the details of how these transformations operate on a
37 
-  \link[GenomicRanges]{GenomicRanges} or \link[GenomicRanges]{GRangesList}
38 
-  object.
29 
+  This man page documents the \emph{intra range transformations} that are
30 
+  supported on \link{RangedSummarizedExperiment} objects.
39 31 
 }
40 32
41 33 
 \usage{
... ... 
@@ -84,12 +76,22 @@
84 76 
 }
85 77
86 78 
 \details{
87 
-  Any of these functions performs the following transformation on
88 
-  \link{RangedSummarizedExperiment} object \code{x}:
89 
-\preformatted{rowRanges(x) <- f(rowRanges(x), ...)
79 
+  These transformations operate on the \code{rowRanges} component of the
80 
+  \link{RangedSummarizedExperiment} object, which can be a
81 
+  \link[GenomicRanges]{GenomicRanges} or \link[GenomicRanges]{GRangesList}
82 
+  object.
83 
+
84 
+  More precisely, any of the above functions performs the following
85 
+  transformation on \link{RangedSummarizedExperiment} object \code{x}:
86 
+\preformatted{    rowRanges(x) <- f(rowRanges(x), ...)
90 87 
 }
91 88 
   where \code{f} is the name of the function and \code{...} any additional
92 89 
   arguments passed to it.
90 
+
91 
+  See \code{?\link[GenomicRanges]{shift}} in the \pkg{GenomicRanges}
92 
+  package for the details of how these transformations operate on a
93 
+  \link[GenomicRanges]{GenomicRanges} or \link[GenomicRanges]{GRangesList}
94 
+  object.
93 95 
 }
94 96
95 97 
 \seealso{
Browse code

Add man page for the findOverlaps family of methods for RangedSummarizedExperiment objects.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SummarizedExperiment@103856 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 15/05/2015 01:00:53
Showing 1 changed files
man/intra-range-methods.Rd
History View file @ e061457
... ... 
@@ -28,12 +28,14 @@
28 28 
 \description{
29 29 
   This man page documents \emph{intra range transformations} of a
30 30 
   \link{RangedSummarizedExperiment} object. These transformations
31 
-  operate on the \code{rowRanges} component of the object.
31 
+  operate on the \code{rowRanges} component of the object, which can be a
32 
+  \link[GenomicRanges]{GenomicRanges} or \link[GenomicRanges]{GRangesList}
33 
+  object.
32 34
33 
-  See \code{?`\link[GenomicRanges]{intra-range-methods}`} in the
34 
-  \pkg{GenomicRanges} package for intra range transformations of a
35 
+  See \code{?\link[GenomicRanges]{shift}} in the \pkg{GenomicRanges}
36 
+  package for the details of how these transformations operate on a
35 37 
   \link[GenomicRanges]{GenomicRanges} or \link[GenomicRanges]{GRangesList}
36 
-  object, which the transformations described below are based on.
38 
+  object.
37 39 
 }
38 40
39 41 
 \usage{
... ... 
@@ -60,24 +62,24 @@
60 62 
     A \link{RangedSummarizedExperiment} object.
61 63 
   }
62 64 
   \item{shift, use.names}{
63 
-    See \code{?`\link[GenomicRanges]{intra-range-methods}`} in the
64 
-    \pkg{GenomicRanges} package.
65 
+    See \code{?\link[GenomicRanges]{shift}} in the \pkg{GenomicRanges}
66 
+    package.
65 67 
   }
66 68 
   \item{start, end, width, fix}{
67 
-    See \code{?`\link[GenomicRanges]{intra-range-methods}`} in the
68 
-    \pkg{GenomicRanges} package.
69 
+    See \code{?\link[GenomicRanges]{shift}} in the \pkg{GenomicRanges}
70 
+    package.
69 71 
   }
70 72 
   \item{ignore.strand, both}{
71 
-    See \code{?`\link[GenomicRanges]{intra-range-methods}`} in the
72 
-    \pkg{GenomicRanges} package.
73 
+    See \code{?\link[GenomicRanges]{shift}} in the \pkg{GenomicRanges}
74 
+    package.
73 75 
   }
74 76 
   \item{upstream, downstream}{
75 
-    See \code{?`\link[GenomicRanges]{intra-range-methods}`} in the
76 
-    \pkg{GenomicRanges} package.
77 
+    See \code{?\link[GenomicRanges]{shift}} in the \pkg{GenomicRanges}
78 
+    package.
77 79 
   }
78 80 
   \item{keep.all.ranges}{
79 
-    See \code{?`\link[GenomicRanges]{intra-range-methods}`} in the
80 
-    \pkg{GenomicRanges} package.
81 
+    See \code{?\link[GenomicRanges]{shift}} in the \pkg{GenomicRanges}
82 
+    package.
81 83 
   }
82 84 
 }
83 85
... ... 
@@ -90,16 +92,14 @@
90 92 
   arguments passed to it.
91 93 
 }
92 94
93 
-\value{
94 
-  See \code{?`\link[GenomicRanges]{intra-range-methods}`} in the
95 
-  \pkg{GenomicRanges} package.
96 
-}
97 
-
98 95 
 \seealso{
99 96 
   \itemize{
100 97 
     \item \link{RangedSummarizedExperiment} objects.
101 
-    \item The \link[GenomicRanges]{intra-range-methods} man page in the
102 
-          \pkg{GenomicRanges} package.
98 
+
99 
+    \item The \link[GenomicRanges]{shift} man page in the
100 
+          \pkg{GenomicRanges} package where \emph{intra range transformations}
101 
+          of a \link[GenomicRanges]{GenomicRanges} or
102 
+          \link[GenomicRanges]{GRangesList} object are documented.
103 103 
   }
104 104 
 }
105 105
Browse code

add man page for "coverage" method

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SummarizedExperiment@103847 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 14/05/2015 23:27:33
Showing 1 changed files
man/intra-range-methods.Rd
History View file @ 07fbcfb
... ... 
@@ -90,6 +90,11 @@
90 90 
   arguments passed to it.
91 91 
 }
92 92
93 
+\value{
94 
+  See \code{?`\link[GenomicRanges]{intra-range-methods}`} in the
95 
+  \pkg{GenomicRanges} package.
96 
+}
97 
+
93 98 
 \seealso{
94 99 
   \itemize{
95 100 
     \item \link{RangedSummarizedExperiment} objects.
Browse code

add man page for inter range methods

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SummarizedExperiment@103846 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 14/05/2015 23:11:21
Showing 1 changed files
man/intra-range-methods.Rd
History View file @ 5bea390
... ... 
@@ -87,7 +87,7 @@
87 87 
 \preformatted{rowRanges(x) <- f(rowRanges(x), ...)
88 88 
 }
89 89 
   where \code{f} is the name of the function and \code{...} any additional
90 
-  arguments passed to the function.
90 
+  arguments passed to it.
91 91 
 }
92 92
93 93 
 \seealso{
Browse code

Add the following methods for RangedSummarizedExperiment objects: (a) intra range transformations, (b) coverage, (c) findOverlaps & family, (d) nearest & family. No man page yet for (b), (c), and (d) (will come soon).

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SummarizedExperiment@103556 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 08/05/2015 08:05:05
Showing 1 changed files
man/intra-range-methods.Rd
History View file @ 6b1f41f
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,144 @@
1 
+\name{intra-range-methods}
2 
+
3 
+\alias{intra-range-methods}
4 
+
5 
+\alias{shift}
6 
+\alias{shift,RangedSummarizedExperiment-method}
7 
+
8 
+\alias{narrow}
9 
+\alias{narrow,RangedSummarizedExperiment-method}
10 
+
11 
+\alias{resize}
12 
+\alias{resize,RangedSummarizedExperiment-method}
13 
+
14 
+\alias{flank}
15 
+\alias{flank,RangedSummarizedExperiment-method}
16 
+
17 
+\alias{promoters}
18 
+\alias{promoters,RangedSummarizedExperiment-method}
19 
+
20 
+\alias{restrict}
21 
+\alias{restrict,RangedSummarizedExperiment-method}
22 
+
23 
+\alias{trim,RangedSummarizedExperiment-method}
24 
+
25 
+
26 
+\title{Intra range transformations of a RangedSummarizedExperiment object}
27 
+
28 
+\description{
29 
+  This man page documents \emph{intra range transformations} of a
30 
+  \link{RangedSummarizedExperiment} object. These transformations
31 
+  operate on the \code{rowRanges} component of the object.
32 
+
33 
+  See \code{?`\link[GenomicRanges]{intra-range-methods}`} in the
34 
+  \pkg{GenomicRanges} package for intra range transformations of a
35 
+  \link[GenomicRanges]{GenomicRanges} or \link[GenomicRanges]{GRangesList}
36 
+  object, which the transformations described below are based on.
37 
+}
38 
+
39 
+\usage{
40 
+\S4method{shift}{RangedSummarizedExperiment}(x, shift=0L, use.names=TRUE)
41 
+
42 
+\S4method{narrow}{RangedSummarizedExperiment}(x, start=NA, end=NA, width=NA, use.names=TRUE)
43 
+
44 
+\S4method{resize}{RangedSummarizedExperiment}(x, width, fix="start", use.names=TRUE,
45 
+       ignore.strand=FALSE)
46 
+
47 
+\S4method{flank}{RangedSummarizedExperiment}(x, width, start=TRUE, both=FALSE,
48 
+      use.names=TRUE, ignore.strand=FALSE)
49 
+
50 
+\S4method{promoters}{RangedSummarizedExperiment}(x, upstream=2000, downstream=200)
51 
+
52 
+\S4method{restrict}{RangedSummarizedExperiment}(x, start=NA, end=NA, keep.all.ranges=FALSE,
53 
+         use.names=TRUE)
54 
+
55 
+\S4method{trim}{RangedSummarizedExperiment}(x, use.names=TRUE)
56 
+}
57 
+
58 
+\arguments{
59 
+  \item{x}{
60 
+    A \link{RangedSummarizedExperiment} object.
61 
+  }
62 
+  \item{shift, use.names}{
63 
+    See \code{?`\link[GenomicRanges]{intra-range-methods}`} in the
64 
+    \pkg{GenomicRanges} package.
65 
+  }
66 
+  \item{start, end, width, fix}{
67 
+    See \code{?`\link[GenomicRanges]{intra-range-methods}`} in the
68 
+    \pkg{GenomicRanges} package.
69 
+  }
70 
+  \item{ignore.strand, both}{
71 
+    See \code{?`\link[GenomicRanges]{intra-range-methods}`} in the
72 
+    \pkg{GenomicRanges} package.
73 
+  }
74 
+  \item{upstream, downstream}{
75 
+    See \code{?`\link[GenomicRanges]{intra-range-methods}`} in the
76 
+    \pkg{GenomicRanges} package.
77 
+  }
78 
+  \item{keep.all.ranges}{
79 
+    See \code{?`\link[GenomicRanges]{intra-range-methods}`} in the
80 
+    \pkg{GenomicRanges} package.
81 
+  }
82 
+}
83 
+
84 
+\details{
85 
+  Any of these functions performs the following transformation on
86 
+  \link{RangedSummarizedExperiment} object \code{x}:
87 
+\preformatted{rowRanges(x) <- f(rowRanges(x), ...)
88 
+}
89 
+  where \code{f} is the name of the function and \code{...} any additional
90 
+  arguments passed to the function.
91 
+}
92 
+
93 
+\seealso{
94 
+  \itemize{
95 
+    \item \link{RangedSummarizedExperiment} objects.
96 
+    \item The \link[GenomicRanges]{intra-range-methods} man page in the
97 
+          \pkg{GenomicRanges} package.
98 
+  }
99 
+}
100 
+
101 
+\examples{
102 
+nrows <- 20; ncols <- 6
103 
+counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
104 
+rowRanges <- GRanges(rep(c("chr1", "chr2"), c(5, 15)),
105 
+                     IRanges(sample(1000L, 20), width=100),
106 
+                     strand=Rle(c("+", "-"), c(12, 8)))
107 
+colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
108 
+                     row.names=LETTERS[1:6])
109 
+se0 <- SummarizedExperiment(assays=SimpleList(counts=counts),
110 
+                            rowRanges=rowRanges, colData=colData)
111 
+
112 
+se1 <- shift(se0, 1)
113 
+stopifnot(identical(
114 
+  rowRanges(se1),
115 
+  shift(rowRanges(se0), 1)
116 
+))
117 
+
118 
+se2 <- narrow(se0, start=10, end=-15)
119 
+stopifnot(identical(
120 
+  rowRanges(se2),
121 
+  narrow(rowRanges(se0), start=10, end=-15)
122 
+))
123 
+
124 
+se3 <- resize(se0, width=75)
125 
+stopifnot(identical(
126 
+  rowRanges(se3),
127 
+  resize(rowRanges(se0), width=75)
128 
+))
129 
+
130 
+se4 <- flank(se0, width=20)
131 
+stopifnot(identical(
132 
+  rowRanges(se4),
133 
+  flank(rowRanges(se0), width=20)
134 
+))
135 
+
136 
+se5 <- restrict(se0, start=200, end=700, keep.all.ranges=TRUE)
137 
+stopifnot(identical(
138 
+  rowRanges(se5),
139 
+  restrict(rowRanges(se0), start=200, end=700, keep.all.ranges=TRUE)
140 
+))
141 
+}
142 
+
143 
+\keyword{methods}
144 
+\keyword{utilities}