1. bsseq
  2. R
  3. hasGRanges.R
Browse code

Repair subsetByOverlaps() on hasGRanges derivatives

Also add overlapsAny() methods and improve granges() method for
hasGRanges derivatives.

Hervé Pagès authored on 20/05/2020 22:23:58
Showing 1 changed files
R/hasGRanges.R
History View file @ 659aee2
... ... 
@@ -7,9 +7,7 @@ setMethod("seqnames", signature(x = "hasGRanges"), function(x) {
7 7 
     seqnames(x@gr)
8 8 
 })
9 9 
 setReplaceMethod("seqnames", "hasGRanges", function(x, value) {
10 
-    gr <- granges(x)
11 
-    seqnames(gr) <- value
12 
-    x@gr <- gr
10 
+    seqnames(x@gr) <- value
13 11 
     x
14 12 
 })
15 13
... ... 
@@ -17,9 +15,7 @@ setMethod("seqlevels", signature(x = "hasGRanges"), function(x) {
17 15 
     seqlevels(x@gr)
18 16 
 })
19 17 
 setReplaceMethod("seqlevels", "hasGRanges", function(x, value) {
20 
-    gr <- granges(x)
21 
-    seqlevels(gr) <- value
22 
-    x@gr <- gr
18 
+    seqlevels(x@gr) <- value
23 19 
     x
24 20 
 })
25 21
... ... 
@@ -27,14 +23,14 @@ setMethod("seqlengths", signature(x = "hasGRanges"), function(x) {
27 23 
     seqlengths(x@gr)
28 24 
 })
29 25 
 setReplaceMethod("seqlengths", "hasGRanges", function(x, value) {
30 
-    gr <- granges(x)
31 
-    seqlengths(gr) <- value
32 
-    x@gr <- gr
26 
+    seqlengths(x@gr) <- value
33 27 
     x
34 28 
 })
35 29
36 30 
 setMethod("granges", signature(x = "hasGRanges"),
37 
-          function(x) x@gr)
31 
+    function(x, use.names = TRUE, use.mcols = FALSE, ...)
32 
+        granges(x@gr, use.names = use.names, use.mcols = use.mcols, ...)
33 
+)
38 34
39 35 
 ## FIXME: might want a granges replacement function
40 36
... ... 
@@ -42,9 +38,7 @@ setMethod("start", "hasGRanges", function(x, ...) {
42 38 
     start(x@gr, ...)
43 39 
 })
44 40 
 setReplaceMethod("start", "hasGRanges", function(x, check = TRUE, value) {
45 
-    gr <- granges(x)
46 
-    start(gr, check = check) <- value
47 
-    x@gr <- gr
41 
+    start(x@gr, check = check) <- value
48 42 
     x
49 43 
 })
50 44
... ... 
@@ -52,9 +46,7 @@ setMethod("end", "hasGRanges", function(x, ...) {
52 46 
     end(x@gr, ...)
53 47 
 })
54 48 
 setReplaceMethod("end", "hasGRanges", function(x, check = TRUE, value) {
55 
-    gr <- granges(x)
56 
-    end(gr, check = check) <- value
57 
-    x@gr <- gr
49 
+    end(x@gr, check = check) <- value
58 50 
     x
59 51 
 })
60 52
... ... 
@@ -62,9 +54,7 @@ setMethod("width", "hasGRanges", function(x) {
62 54 
     width(x@gr)
63 55 
 })
64 56 
 setReplaceMethod("width", "hasGRanges", function(x, check = TRUE, value) {
65 
-    gr <- granges(x)
66 
-    width(gr, check = check) <- value
67 
-    x@gr <- gr
57 
+    width(x@gr, check = check) <- value
68 58 
     x
69 59 
 })
70 60
... ... 
@@ -72,49 +62,20 @@ setMethod("strand", "hasGRanges", function(x) {
72 62 
     strand(x@gr)
73 63 
 })
74 64 
 setReplaceMethod("strand", "hasGRanges", function(x, value) {
75 
-    gr <- granges(x)
76 
-    strand(gr) <- value
77 
-    x@gr <- gr
65 
+    strand(x@gr) <- value
78 66 
     x
79 67 
 })
80 68
81 69 
 setMethod("length", "hasGRanges", function(x) length(x@gr))
82 70
83 
-## setMethod("subsetByOverlaps",
84 
-##           signature(query = "hasGRanges", subject = "GenomicRanges"),
85 
-##           function(query, subject, maxgap = 0L, minoverlap = 1L,
86 
-##                    type = c("any", "start", "end", "within", "equal"),
87 
-##                    ignore.strand = FALSE, ...) {
88 
-##               ov <- findOverlaps(query = granges(query), subject = subject,
89 
-##                                  maxgap = maxgap, minoverlap = minoverlap,
90 
-##                                  type = match.arg(type), select = "arbitrary",
91 
-##                                  ignore.strand = ignore.strand, ... )
92 
-##               query[!is.na(ov)]
93 
-##           })
94 
-
95 
-## setMethod("subsetByOverlaps",
96 
-##           signature(query = "hasGRanges", subject = "hasGRanges"),
97 
-##           function(query, subject, maxgap = 0L, minoverlap = 1L,
98 
-##                    type = c("any", "start", "end", "within", "equal"),
99 
-##                    ignore.strand = FALSE, ...) {
100 
-##               ov <- findOverlaps(query = granges(query), subject = granges(subject),
101 
-##                                  maxgap = maxgap, minoverlap = minoverlap,
102 
-##                                  type = match.arg(type), select = "arbitrary",
103 
-##                                  ignore.strand = ignore.strand, ... )
104 
-##               query[!is.na(ov)]
105 
-##           })
106 
-
107 
-## setMethod("subsetByOverlaps",
108 
-##           signature(query = "GenomicRanges", subject = "hasGRanges"),
109 
-##           function(query, subject, maxgap = 0L, minoverlap = 1L,
110 
-##                    type = c("any", "start", "end", "within", "equal"),
111 
-##                    ignore.strand = FALSE, ...) {
112 
-##               ov <- findOverlaps(query = query, subject = granges(subject),
113 
-##                                  maxgap = maxgap, minoverlap = minoverlap,
114 
-##                                  type = match.arg(type), select = "arbitrary",
115 
-##                                  ignore.strand = ignore.strand, ... )
116 
-##               query[!is.na(ov)]
117 
-##           })
71 
+setMethod("[", "hasGRanges", function(x, i, ...) {
72 
+    if(missing(i))
73 
+        stop("need [i] for subsetting")
74 
+    if(missing(i))
75 
+        return(x)
76 
+    x@gr <- x@gr[i]
77 
+    x
78 
+})
118 79
119 80 
 setMethod("findOverlaps",
120 81 
           signature(query = "hasGRanges", subject = "GenomicRanges"),
... ... 
@@ -122,42 +83,53 @@ setMethod("findOverlaps",
122 83 
                     type = c("any", "start", "end", "within", "equal"),
123 84 
                     select = c("all", "first", "last", "arbitrary"),
124 85 
                     ignore.strand = FALSE, ...) {
125 
-              findOverlaps(query = granges(query), subject = subject,
86 
+              findOverlaps(query = query@gr, subject = subject,
126 87 
                            maxgap = maxgap, minoverlap = minoverlap,
127 88 
                            type = match.arg(type), select = match.arg(select),
128 89 
                            ignore.strand = ignore.strand, ...)
129 90 
           })
130 91
131 92 
 setMethod("findOverlaps",
132 
-          signature(query = "hasGRanges", subject = "hasGRanges"),
93 
+          signature(query = "GenomicRanges", subject = "hasGRanges"),
133 94 
           function (query, subject, maxgap = -1L, minoverlap = 0L,
134 95 
                     type = c("any", "start", "end", "within", "equal"),
135 96 
                     select = c("all", "first", "last", "arbitrary"),
136 97 
                     ignore.strand = FALSE, ...) {
137 
-              findOverlaps(query = granges(query), subject = granges(subject),
98 
+              findOverlaps(query = query, subject = subject@gr,
138 99 
                            maxgap = maxgap, minoverlap = minoverlap,
139 100 
                            type = match.arg(type), select = match.arg(select),
140 101 
                            ignore.strand = ignore.strand, ...)
141 102 
           })
142 103
143 104 
 setMethod("findOverlaps",
144 
-          signature(query = "GenomicRanges", subject = "hasGRanges"),
105 
+          signature(query = "hasGRanges", subject = "hasGRanges"),
145 106 
           function (query, subject, maxgap = -1L, minoverlap = 0L,
146 107 
                     type = c("any", "start", "end", "within", "equal"),
147 108 
                     select = c("all", "first", "last", "arbitrary"),
148 109 
                     ignore.strand = FALSE, ...) {
149 
-              findOverlaps(query = query, subject = granges(subject),
110 
+              findOverlaps(query = query@gr, subject = subject@gr,
150 111 
                            maxgap = maxgap, minoverlap = minoverlap,
151 112 
                            type = match.arg(type), select = match.arg(select),
152 113 
                            ignore.strand = ignore.strand, ...)
153 114 
           })
154 115
155 
-setMethod("[", "hasGRanges", function(x, i, ...) {
156 
-    if(missing(i))
157 
-        stop("need [i] for subsetting")
158 
-    if(missing(i))
159 
-        return(x)
160 
-    x@gr <- x@gr[i]
161 
-    x
162 
-})
116 
+setMethod("overlapsAny", c("hasGRanges", "GenomicRanges"),
117 
+    IRanges:::default_overlapsAny
118 
+)
119 
+setMethod("overlapsAny", c("GenomicRanges", "hasGRanges"),
120 
+    IRanges:::default_overlapsAny
121 
+)
122 
+setMethod("overlapsAny", c("hasGRanges", "hasGRanges"),
123 
+    IRanges:::default_overlapsAny
124 
+)
125 
+
126 
+setMethod("subsetByOverlaps", c("hasGRanges", "GenomicRanges"),
127 
+    IRanges:::default_subsetByOverlaps
128 
+)
129 
+setMethod("subsetByOverlaps", c("GenomicRanges", "hasGRanges"),
130 
+    IRanges:::default_subsetByOverlaps
131 
+)
132 
+setMethod("subsetByOverlaps", c("hasGRanges", "hasGRanges"),
133 
+    IRanges:::default_subsetByOverlaps
134 
+)
163 135
Browse code

resolving conflicts:

Kasper Daniel Hansen authored on 16/10/2017 18:53:15
Showing 0 changed files
Browse code

- Use new 'maxgap' and 'minoverlap' defaults in "findOverlaps" method for hasGRanges objects. - Remove "subsetByOverlaps" methods for hasGRanges objects. They are redundant with the default "subsetByOverlaps" method defined in the IRanges package. The default method works out-of-the-box on any object that supports findOverlaps() and linear subsetting ([), which is the case for hasGRanges objects.

Hervé Pagès authored on 18/09/2017 15:02:27
Showing 1 changed files
R/hasGRanges.R
History View file @ 8f4b326
... ... 
@@ -81,45 +81,9 @@ setReplaceMethod("strand", "hasGRanges", function(x, value) {
81 81 
 setMethod("length", "hasGRanges", function(x) length(x@gr))
82 82
83 83
84 
-setMethod("subsetByOverlaps",
85 
-          signature(query = "hasGRanges", subject = "GenomicRanges"),
86 
-          function(query, subject, maxgap = 0L, minoverlap = 1L,
87 
-                   type = c("any", "start", "end", "within", "equal"),
88 
-                   ignore.strand = FALSE, ...) {
89 
-              ov <- findOverlaps(query = granges(query), subject = subject,
90 
-                                 maxgap = maxgap, minoverlap = minoverlap,
91 
-                                 type = match.arg(type), select = "arbitrary",
92 
-                                 ignore.strand = ignore.strand, ... )
93 
-              query[!is.na(ov)]
94 
-          })
95 
-
96 
-setMethod("subsetByOverlaps",
97 
-          signature(query = "hasGRanges", subject = "hasGRanges"),
98 
-          function(query, subject, maxgap = 0L, minoverlap = 1L,
99 
-                   type = c("any", "start", "end", "within", "equal"),
100 
-                   ignore.strand = FALSE, ...) {
101 
-              ov <- findOverlaps(query = granges(query), subject = granges(subject),
102 
-                                 maxgap = maxgap, minoverlap = minoverlap,
103 
-                                 type = match.arg(type), select = "arbitrary",
104 
-                                 ignore.strand = ignore.strand, ... )
105 
-              query[!is.na(ov)]
106 
-          })
107 
-
108 
-setMethod("subsetByOverlaps",
109 
-          signature(query = "GenomicRanges", subject = "hasGRanges"),
110 
-          function(query, subject, maxgap = 0L, minoverlap = 1L,
111 
-                   type = c("any", "start", "end", "within", "equal"),
112 
-                   ignore.strand = FALSE, ...) {
113 
-              ov <- findOverlaps(query = query, subject = granges(subject),
114 
-                                 maxgap = maxgap, minoverlap = minoverlap,
115 
-                                 type = match.arg(type), select = "arbitrary",
116 
-                                 ignore.strand = ignore.strand, ... )
117 
-              query[!is.na(ov)]
118 
-          })
119 
-
120 84 
 setMethod("findOverlaps",
121 85 
           signature(query = "hasGRanges", subject = "GenomicRanges"),
122 
-          function (query, subject, maxgap = 0L, minoverlap = 1L,
86 
+          function (query, subject, maxgap = -1L, minoverlap = 0L,
123 87 
                     type = c("any", "start", "end", "within", "equal"),
124 88 
                     select = c("all", "first", "last", "arbitrary"),
125 89 
                     ignore.strand = FALSE, ...) {
... ... 
@@ -131,7 +95,7 @@ setMethod("findOverlaps",
131 95
132 96 
 setMethod("findOverlaps",
133 97 
           signature(query = "hasGRanges", subject = "hasGRanges"),
134 
-          function (query, subject, maxgap = 0L, minoverlap = 1L,
98 
+          function (query, subject, maxgap = -1L, minoverlap = 0L,
135 99 
                     type = c("any", "start", "end", "within", "equal"),
136 100 
                     select = c("all", "first", "last", "arbitrary"),
137 101 
                     ignore.strand = FALSE, ...) {
... ... 
@@ -143,7 +107,7 @@ setMethod("findOverlaps",
143 107
144 108 
 setMethod("findOverlaps",
145 109 
           signature(query = "GenomicRanges", subject = "hasGRanges"),
146 
-          function (query, subject, maxgap = 0L, minoverlap = 1L,
110 
+          function (query, subject, maxgap = -1L, minoverlap = 0L,
147 111 
                     type = c("any", "start", "end", "within", "equal"),
148 112 
                     select = c("all", "first", "last", "arbitrary"),
149 113 
                     ignore.strand = FALSE, ...) {
Browse code

merge conflicts

From: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@114581 bc3139a8-67e5-0310-9ffc-ced21a209358

Kasper D. Hansen authored on 10/03/2016 02:44:17
Showing 1 changed files
R/hasGRanges.R
History View file @ 5e9d3da
... ... 
@@ -121,7 +121,7 @@ setMethod("findOverlaps",
121 121 
           signature(query = "hasGRanges", subject = "GenomicRanges"),
122 122 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
123 123 
                     type = c("any", "start", "end", "within", "equal"),
124 
-                    select = c("all", "first"),
124 
+                    select = c("all", "first", "last", "arbitrary"),
125 125 
                     ignore.strand = FALSE, ...) {
126 126 
               findOverlaps(query = granges(query), subject = subject,
127 127 
                            maxgap = maxgap, minoverlap = minoverlap,
... ... 
@@ -133,7 +133,7 @@ setMethod("findOverlaps",
133 133 
           signature(query = "hasGRanges", subject = "hasGRanges"),
134 134 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
135 135 
                     type = c("any", "start", "end", "within", "equal"),
136 
-                    select = c("all", "first"),
136 
+                    select = c("all", "first", "last", "arbitrary"),
137 137 
                     ignore.strand = FALSE, ...) {
138 138 
               findOverlaps(query = granges(query), subject = granges(subject),
139 139 
                            maxgap = maxgap, minoverlap = minoverlap,
... ... 
@@ -145,7 +145,7 @@ setMethod("findOverlaps",
145 145 
           signature(query = "GenomicRanges", subject = "hasGRanges"),
146 146 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
147 147 
                     type = c("any", "start", "end", "within", "equal"),
148 
-                    select = c("all", "first"),
148 
+                    select = c("all", "first", "last", "arbitrary"),
149 149 
                     ignore.strand = FALSE, ...) {
150 150 
               findOverlaps(query = query, subject = granges(subject),
151 151 
                            maxgap = maxgap, minoverlap = minoverlap,
Browse code

merge conflicts

From: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@114581 bc3139a8-67e5-0310-9ffc-ced21a209358

khansen authored on 10/03/2016 02:44:17
Showing 1 changed files
R/hasGRanges.R
History View file @ 8657761
... ... 
@@ -121,7 +121,7 @@ setMethod("findOverlaps",
121 121 
           signature(query = "hasGRanges", subject = "GenomicRanges"),
122 122 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
123 123 
                     type = c("any", "start", "end", "within", "equal"),
124 
-                    select = c("all", "first"),
124 
+                    select = c("all", "first", "last", "arbitrary"),
125 125 
                     ignore.strand = FALSE, ...) {
126 126 
               findOverlaps(query = granges(query), subject = subject,
127 127 
                            maxgap = maxgap, minoverlap = minoverlap,
... ... 
@@ -133,7 +133,7 @@ setMethod("findOverlaps",
133 133 
           signature(query = "hasGRanges", subject = "hasGRanges"),
134 134 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
135 135 
                     type = c("any", "start", "end", "within", "equal"),
136 
-                    select = c("all", "first"),
136 
+                    select = c("all", "first", "last", "arbitrary"),
137 137 
                     ignore.strand = FALSE, ...) {
138 138 
               findOverlaps(query = granges(query), subject = granges(subject),
139 139 
                            maxgap = maxgap, minoverlap = minoverlap,
... ... 
@@ -145,7 +145,7 @@ setMethod("findOverlaps",
145 145 
           signature(query = "GenomicRanges", subject = "hasGRanges"),
146 146 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
147 147 
                     type = c("any", "start", "end", "within", "equal"),
148 
-                    select = c("all", "first"),
148 
+                    select = c("all", "first", "last", "arbitrary"),
149 149 
                     ignore.strand = FALSE, ...) {
150 150 
               findOverlaps(query = query, subject = granges(subject),
151 151 
                            maxgap = maxgap, minoverlap = minoverlap,
Browse code

findOverlaps() and subsetByOverlaps() have no 'algorithm' argument anymore

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@111565 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 16/12/2015 21:21:51
Showing 1 changed files
R/hasGRanges.R
History View file @ a4efefe
... ... 
@@ -85,12 +85,10 @@ setMethod("subsetByOverlaps",
85 85 
           signature(query = "hasGRanges", subject = "GenomicRanges"),
86 86 
           function(query, subject, maxgap = 0L, minoverlap = 1L,
87 87 
                    type = c("any", "start", "end", "within", "equal"),
88 
-                   algorithm = c("nclist", "intervaltree"),
89 88 
                    ignore.strand = FALSE, ...) {
90 89 
               ov <- findOverlaps(query = granges(query), subject = subject,
91 90 
                                  maxgap = maxgap, minoverlap = minoverlap,
92 91 
                                  type = match.arg(type), select = "arbitrary",
93 
-                                 algorithm = match.arg(algorithm),
94 92 
                                  ignore.strand = ignore.strand, ... )
95 93 
               query[!is.na(ov)]
96 94 
           })
... ... 
@@ -99,12 +97,10 @@ setMethod("subsetByOverlaps",
99 97 
           signature(query = "hasGRanges", subject = "hasGRanges"),
100 98 
           function(query, subject, maxgap = 0L, minoverlap = 1L,
101 99 
                    type = c("any", "start", "end", "within", "equal"),
102 
-                   algorithm = c("nclist", "intervaltree"),
103 100 
                    ignore.strand = FALSE, ...) {
104 101 
               ov <- findOverlaps(query = granges(query), subject = granges(subject),
105 102 
                                  maxgap = maxgap, minoverlap = minoverlap,
106 103 
                                  type = match.arg(type), select = "arbitrary",
107 
-                                 algorithm = match.arg(algorithm),
108 104 
                                  ignore.strand = ignore.strand, ... )
109 105 
               query[!is.na(ov)]
110 106 
           })
... ... 
@@ -113,12 +109,10 @@ setMethod("subsetByOverlaps",
113 109 
           signature(query = "GenomicRanges", subject = "hasGRanges"),
114 110 
           function(query, subject, maxgap = 0L, minoverlap = 1L,
115 111 
                    type = c("any", "start", "end", "within", "equal"),
116 
-                   algorithm = c("nclist", "intervaltree"),
117 112 
                    ignore.strand = FALSE, ...) {
118 113 
               ov <- findOverlaps(query = query, subject = granges(subject),
119 114 
                                  maxgap = maxgap, minoverlap = minoverlap,
120 115 
                                  type = match.arg(type), select = "arbitrary",
121 
-                                 algorithm = match.arg(algorithm),
122 116 
                                  ignore.strand = ignore.strand, ... )
123 117 
               query[!is.na(ov)]
124 118 
           })
... ... 
@@ -128,12 +122,10 @@ setMethod("findOverlaps",
128 122 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
129 123 
                     type = c("any", "start", "end", "within", "equal"),
130 124 
                     select = c("all", "first"),
131 
-                    algorithm = c("nclist", "intervaltree"),
132 125 
                     ignore.strand = FALSE, ...) {
133 126 
               findOverlaps(query = granges(query), subject = subject,
134 127 
                            maxgap = maxgap, minoverlap = minoverlap,
135 128 
                            type = match.arg(type), select = match.arg(select),
136 
-                           algorithm = match.arg(algorithm),
137 129 
                            ignore.strand = ignore.strand, ...)
138 130 
           })
139 131
... ... 
@@ -142,12 +134,10 @@ setMethod("findOverlaps",
142 134 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
143 135 
                     type = c("any", "start", "end", "within", "equal"),
144 136 
                     select = c("all", "first"),
145 
-                    algorithm = c("nclist", "intervaltree"),
146 137 
                     ignore.strand = FALSE, ...) {
147 138 
               findOverlaps(query = granges(query), subject = granges(subject),
148 139 
                            maxgap = maxgap, minoverlap = minoverlap,
149 140 
                            type = match.arg(type), select = match.arg(select),
150 
-                           algorithm = match.arg(algorithm),
151 141 
                            ignore.strand = ignore.strand, ...)
152 142 
           })
153 143
... ... 
@@ -156,12 +146,10 @@ setMethod("findOverlaps",
156 146 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
157 147 
                     type = c("any", "start", "end", "within", "equal"),
158 148 
                     select = c("all", "first"),
159 
-                    algorithm = c("nclist", "intervaltree"),
160 149 
                     ignore.strand = FALSE, ...) {
161 150 
               findOverlaps(query = query, subject = granges(subject),
162 151 
                            maxgap = maxgap, minoverlap = minoverlap,
163 152 
                            type = match.arg(type), select = match.arg(select),
164 
-                           algorithm = match.arg(algorithm),
165 153 
                            ignore.strand = ignore.strand, ...)
166 154 
           })
167 155
Browse code

findOverlaps() and subsetByOverlaps() have no 'algorithm' argument anymore

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@111565 bc3139a8-67e5-0310-9ffc-ced21a209358

hpages@fhcrc.org authored on 16/12/2015 21:21:51
Showing 1 changed files
R/hasGRanges.R
History View file @ cc7c8a0
... ... 
@@ -85,12 +85,10 @@ setMethod("subsetByOverlaps",
85 85 
           signature(query = "hasGRanges", subject = "GenomicRanges"),
86 86 
           function(query, subject, maxgap = 0L, minoverlap = 1L,
87 87 
                    type = c("any", "start", "end", "within", "equal"),
88 
-                   algorithm = c("nclist", "intervaltree"),
89 88 
                    ignore.strand = FALSE, ...) {
90 89 
               ov <- findOverlaps(query = granges(query), subject = subject,
91 90 
                                  maxgap = maxgap, minoverlap = minoverlap,
92 91 
                                  type = match.arg(type), select = "arbitrary",
93 
-                                 algorithm = match.arg(algorithm),
94 92 
                                  ignore.strand = ignore.strand, ... )
95 93 
               query[!is.na(ov)]
96 94 
           })
... ... 
@@ -99,12 +97,10 @@ setMethod("subsetByOverlaps",
99 97 
           signature(query = "hasGRanges", subject = "hasGRanges"),
100 98 
           function(query, subject, maxgap = 0L, minoverlap = 1L,
101 99 
                    type = c("any", "start", "end", "within", "equal"),
102 
-                   algorithm = c("nclist", "intervaltree"),
103 100 
                    ignore.strand = FALSE, ...) {
104 101 
               ov <- findOverlaps(query = granges(query), subject = granges(subject),
105 102 
                                  maxgap = maxgap, minoverlap = minoverlap,
106 103 
                                  type = match.arg(type), select = "arbitrary",
107 
-                                 algorithm = match.arg(algorithm),
108 104 
                                  ignore.strand = ignore.strand, ... )
109 105 
               query[!is.na(ov)]
110 106 
           })
... ... 
@@ -113,12 +109,10 @@ setMethod("subsetByOverlaps",
113 109 
           signature(query = "GenomicRanges", subject = "hasGRanges"),
114 110 
           function(query, subject, maxgap = 0L, minoverlap = 1L,
115 111 
                    type = c("any", "start", "end", "within", "equal"),
116 
-                   algorithm = c("nclist", "intervaltree"),
117 112 
                    ignore.strand = FALSE, ...) {
118 113 
               ov <- findOverlaps(query = query, subject = granges(subject),
119 114 
                                  maxgap = maxgap, minoverlap = minoverlap,
120 115 
                                  type = match.arg(type), select = "arbitrary",
121 
-                                 algorithm = match.arg(algorithm),
122 116 
                                  ignore.strand = ignore.strand, ... )
123 117 
               query[!is.na(ov)]
124 118 
           })
... ... 
@@ -128,12 +122,10 @@ setMethod("findOverlaps",
128 122 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
129 123 
                     type = c("any", "start", "end", "within", "equal"),
130 124 
                     select = c("all", "first"),
131 
-                    algorithm = c("nclist", "intervaltree"),
132 125 
                     ignore.strand = FALSE, ...) {
133 126 
               findOverlaps(query = granges(query), subject = subject,
134 127 
                            maxgap = maxgap, minoverlap = minoverlap,
135 128 
                            type = match.arg(type), select = match.arg(select),
136 
-                           algorithm = match.arg(algorithm),
137 129 
                            ignore.strand = ignore.strand, ...)
138 130 
           })
139 131
... ... 
@@ -142,12 +134,10 @@ setMethod("findOverlaps",
142 134 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
143 135 
                     type = c("any", "start", "end", "within", "equal"),
144 136 
                     select = c("all", "first"),
145 
-                    algorithm = c("nclist", "intervaltree"),
146 137 
                     ignore.strand = FALSE, ...) {
147 138 
               findOverlaps(query = granges(query), subject = granges(subject),
148 139 
                            maxgap = maxgap, minoverlap = minoverlap,
149 140 
                            type = match.arg(type), select = match.arg(select),
150 
-                           algorithm = match.arg(algorithm),
151 141 
                            ignore.strand = ignore.strand, ...)
152 142 
           })
153 143
... ... 
@@ -156,12 +146,10 @@ setMethod("findOverlaps",
156 146 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
157 147 
                     type = c("any", "start", "end", "within", "equal"),
158 148 
                     select = c("all", "first"),
159 
-                    algorithm = c("nclist", "intervaltree"),
160 149 
                     ignore.strand = FALSE, ...) {
161 150 
               findOverlaps(query = query, subject = granges(subject),
162 151 
                            maxgap = maxgap, minoverlap = minoverlap,
163 152 
                            type = match.arg(type), select = match.arg(select),
164 
-                           algorithm = match.arg(algorithm),
165 153 
                            ignore.strand = ignore.strand, ...)
166 154 
           })
167 155
Browse code

add 'algorithm' arg to "subsetByOverlaps" methods

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@97407 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 05/12/2014 06:42:18
Showing 1 changed files
R/hasGRanges.R
History View file @ c651329
... ... 
@@ -85,10 +85,12 @@ setMethod("subsetByOverlaps",
85 85 
           signature(query = "hasGRanges", subject = "GenomicRanges"),
86 86 
           function(query, subject, maxgap = 0L, minoverlap = 1L,
87 87 
                    type = c("any", "start", "end", "within", "equal"),
88 
+                   algorithm = c("nclist", "intervaltree"),
88 89 
                    ignore.strand = FALSE, ...) {
89 90 
               ov <- findOverlaps(query = granges(query), subject = subject,
90 91 
                                  maxgap = maxgap, minoverlap = minoverlap,
91 
-                                 type = match.arg(type), select = "first",
92 
+                                 type = match.arg(type), select = "arbitrary",
93 
+                                 algorithm = match.arg(algorithm),
92 94 
                                  ignore.strand = ignore.strand, ... )
93 95 
               query[!is.na(ov)]
94 96 
           })
... ... 
@@ -97,10 +99,12 @@ setMethod("subsetByOverlaps",
97 99 
           signature(query = "hasGRanges", subject = "hasGRanges"),
98 100 
           function(query, subject, maxgap = 0L, minoverlap = 1L,
99 101 
                    type = c("any", "start", "end", "within", "equal"),
102 
+                   algorithm = c("nclist", "intervaltree"),
100 103 
                    ignore.strand = FALSE, ...) {
101 104 
               ov <- findOverlaps(query = granges(query), subject = granges(subject),
102 105 
                                  maxgap = maxgap, minoverlap = minoverlap,
103 
-                                 type = match.arg(type), select = "first",
106 
+                                 type = match.arg(type), select = "arbitrary",
107 
+                                 algorithm = match.arg(algorithm),
104 108 
                                  ignore.strand = ignore.strand, ... )
105 109 
               query[!is.na(ov)]
106 110 
           })
... ... 
@@ -109,10 +113,12 @@ setMethod("subsetByOverlaps",
109 113 
           signature(query = "GenomicRanges", subject = "hasGRanges"),
110 114 
           function(query, subject, maxgap = 0L, minoverlap = 1L,
111 115 
                    type = c("any", "start", "end", "within", "equal"),
116 
+                   algorithm = c("nclist", "intervaltree"),
112 117 
                    ignore.strand = FALSE, ...) {
113 118 
               ov <- findOverlaps(query = query, subject = granges(subject),
114 119 
                                  maxgap = maxgap, minoverlap = minoverlap,
115 
-                                 type = match.arg(type), select = "first",
120 
+                                 type = match.arg(type), select = "arbitrary",
121 
+                                 algorithm = match.arg(algorithm),
116 122 
                                  ignore.strand = ignore.strand, ... )
117 123 
               query[!is.na(ov)]
118 124 
           })
Browse code

add 'algorithm' arg to "subsetByOverlaps" methods

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@97407 bc3139a8-67e5-0310-9ffc-ced21a209358

hpages@fhcrc.org authored on 05/12/2014 06:42:18
Showing 1 changed files
R/hasGRanges.R
History View file @ 0a6cbe0
... ... 
@@ -85,10 +85,12 @@ setMethod("subsetByOverlaps",
85 85 
           signature(query = "hasGRanges", subject = "GenomicRanges"),
86 86 
           function(query, subject, maxgap = 0L, minoverlap = 1L,
87 87 
                    type = c("any", "start", "end", "within", "equal"),
88 
+                   algorithm = c("nclist", "intervaltree"),
88 89 
                    ignore.strand = FALSE, ...) {
89 90 
               ov <- findOverlaps(query = granges(query), subject = subject,
90 91 
                                  maxgap = maxgap, minoverlap = minoverlap,
91 
-                                 type = match.arg(type), select = "first",
92 
+                                 type = match.arg(type), select = "arbitrary",
93 
+                                 algorithm = match.arg(algorithm),
92 94 
                                  ignore.strand = ignore.strand, ... )
93 95 
               query[!is.na(ov)]
94 96 
           })
... ... 
@@ -97,10 +99,12 @@ setMethod("subsetByOverlaps",
97 99 
           signature(query = "hasGRanges", subject = "hasGRanges"),
98 100 
           function(query, subject, maxgap = 0L, minoverlap = 1L,
99 101 
                    type = c("any", "start", "end", "within", "equal"),
102 
+                   algorithm = c("nclist", "intervaltree"),
100 103 
                    ignore.strand = FALSE, ...) {
101 104 
               ov <- findOverlaps(query = granges(query), subject = granges(subject),
102 105 
                                  maxgap = maxgap, minoverlap = minoverlap,
103 
-                                 type = match.arg(type), select = "first",
106 
+                                 type = match.arg(type), select = "arbitrary",
107 
+                                 algorithm = match.arg(algorithm),
104 108 
                                  ignore.strand = ignore.strand, ... )
105 109 
               query[!is.na(ov)]
106 110 
           })
... ... 
@@ -109,10 +113,12 @@ setMethod("subsetByOverlaps",
109 113 
           signature(query = "GenomicRanges", subject = "hasGRanges"),
110 114 
           function(query, subject, maxgap = 0L, minoverlap = 1L,
111 115 
                    type = c("any", "start", "end", "within", "equal"),
116 
+                   algorithm = c("nclist", "intervaltree"),
112 117 
                    ignore.strand = FALSE, ...) {
113 118 
               ov <- findOverlaps(query = query, subject = granges(subject),
114 119 
                                  maxgap = maxgap, minoverlap = minoverlap,
115 
-                                 type = match.arg(type), select = "first",
120 
+                                 type = match.arg(type), select = "arbitrary",
121 
+                                 algorithm = match.arg(algorithm),
116 122 
                                  ignore.strand = ignore.strand, ... )
117 123 
               query[!is.na(ov)]
118 124 
           })
Browse code

change 'algorithm' default from "intervaltree" to "nclist"

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@97403 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 05/12/2014 06:14:38
Showing 1 changed files
R/hasGRanges.R
History View file @ 8f99870
... ... 
@@ -122,7 +122,7 @@ setMethod("findOverlaps",
122 122 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
123 123 
                     type = c("any", "start", "end", "within", "equal"),
124 124 
                     select = c("all", "first"),
125 
-                    algorithm = c("intervaltree", "nclist"),
125 
+                    algorithm = c("nclist", "intervaltree"),
126 126 
                     ignore.strand = FALSE, ...) {
127 127 
               findOverlaps(query = granges(query), subject = subject,
128 128 
                            maxgap = maxgap, minoverlap = minoverlap,
... ... 
@@ -136,7 +136,7 @@ setMethod("findOverlaps",
136 136 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
137 137 
                     type = c("any", "start", "end", "within", "equal"),
138 138 
                     select = c("all", "first"),
139 
-                    algorithm = c("intervaltree", "nclist"),
139 
+                    algorithm = c("nclist", "intervaltree"),
140 140 
                     ignore.strand = FALSE, ...) {
141 141 
               findOverlaps(query = granges(query), subject = granges(subject),
142 142 
                            maxgap = maxgap, minoverlap = minoverlap,
... ... 
@@ -150,7 +150,7 @@ setMethod("findOverlaps",
150 150 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
151 151 
                     type = c("any", "start", "end", "within", "equal"),
152 152 
                     select = c("all", "first"),
153 
-                    algorithm = c("intervaltree", "nclist"),
153 
+                    algorithm = c("nclist", "intervaltree"),
154 154 
                     ignore.strand = FALSE, ...) {
155 155 
               findOverlaps(query = query, subject = granges(subject),
156 156 
                            maxgap = maxgap, minoverlap = minoverlap,
Browse code

change 'algorithm' default from "intervaltree" to "nclist"

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@97403 bc3139a8-67e5-0310-9ffc-ced21a209358

hpages@fhcrc.org authored on 05/12/2014 06:14:38
Showing 1 changed files
R/hasGRanges.R
History View file @ 3fedb39
... ... 
@@ -122,7 +122,7 @@ setMethod("findOverlaps",
122 122 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
123 123 
                     type = c("any", "start", "end", "within", "equal"),
124 124 
                     select = c("all", "first"),
125 
-                    algorithm = c("intervaltree", "nclist"),
125 
+                    algorithm = c("nclist", "intervaltree"),
126 126 
                     ignore.strand = FALSE, ...) {
127 127 
               findOverlaps(query = granges(query), subject = subject,
128 128 
                            maxgap = maxgap, minoverlap = minoverlap,
... ... 
@@ -136,7 +136,7 @@ setMethod("findOverlaps",
136 136 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
137 137 
                     type = c("any", "start", "end", "within", "equal"),
138 138 
                     select = c("all", "first"),
139 
-                    algorithm = c("intervaltree", "nclist"),
139 
+                    algorithm = c("nclist", "intervaltree"),
140 140 
                     ignore.strand = FALSE, ...) {
141 141 
               findOverlaps(query = granges(query), subject = granges(subject),
142 142 
                            maxgap = maxgap, minoverlap = minoverlap,
... ... 
@@ -150,7 +150,7 @@ setMethod("findOverlaps",
150 150 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
151 151 
                     type = c("any", "start", "end", "within", "equal"),
152 152 
                     select = c("all", "first"),
153 
-                    algorithm = c("intervaltree", "nclist"),
153 
+                    algorithm = c("nclist", "intervaltree"),
154 154 
                     ignore.strand = FALSE, ...) {
155 155 
               findOverlaps(query = query, subject = granges(subject),
156 156 
                            maxgap = maxgap, minoverlap = minoverlap,
Browse code

The findOverlaps() generic got a new 'algorithm' argument in IRanges 2.1.10 (commit 96627). So add it to all "findOverlaps" methods defined in bsseq.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@96631 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 08/11/2014 02:53:46
Showing 1 changed files
R/hasGRanges.R
History View file @ 40dc11d
... ... 
@@ -121,10 +121,13 @@ setMethod("findOverlaps",
121 121 
           signature(query = "hasGRanges", subject = "GenomicRanges"),
122 122 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
123 123 
                     type = c("any", "start", "end", "within", "equal"),
124 
-                    select = c("all", "first"), ignore.strand = FALSE, ...) {
124 
+                    select = c("all", "first"),
125 
+                    algorithm = c("intervaltree", "nclist"),
126 
+                    ignore.strand = FALSE, ...) {
125 127 
               findOverlaps(query = granges(query), subject = subject,
126 128 
                            maxgap = maxgap, minoverlap = minoverlap,
127 129 
                            type = match.arg(type), select = match.arg(select),
130 
+                           algorithm = match.arg(algorithm),
128 131 
                            ignore.strand = ignore.strand, ...)
129 132 
           })
130 133
... ... 
@@ -132,10 +135,13 @@ setMethod("findOverlaps",
132 135 
           signature(query = "hasGRanges", subject = "hasGRanges"),
133 136 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
134 137 
                     type = c("any", "start", "end", "within", "equal"),
135 
-                    select = c("all", "first"), ignore.strand = FALSE, ...) {
138 
+                    select = c("all", "first"),
139 
+                    algorithm = c("intervaltree", "nclist"),
140 
+                    ignore.strand = FALSE, ...) {
136 141 
               findOverlaps(query = granges(query), subject = granges(subject),
137 142 
                            maxgap = maxgap, minoverlap = minoverlap,
138 143 
                            type = match.arg(type), select = match.arg(select),
144 
+                           algorithm = match.arg(algorithm),
139 145 
                            ignore.strand = ignore.strand, ...)
140 146 
           })
141 147
... ... 
@@ -143,10 +149,13 @@ setMethod("findOverlaps",
143 149 
           signature(query = "GenomicRanges", subject = "hasGRanges"),
144 150 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
145 151 
                     type = c("any", "start", "end", "within", "equal"),
146 
-                    select = c("all", "first"), ignore.strand = FALSE, ...) {
152 
+                    select = c("all", "first"),
153 
+                    algorithm = c("intervaltree", "nclist"),
154 
+                    ignore.strand = FALSE, ...) {
147 155 
               findOverlaps(query = query, subject = granges(subject),
148 156 
                            maxgap = maxgap, minoverlap = minoverlap,
149 157 
                            type = match.arg(type), select = match.arg(select),
158 
+                           algorithm = match.arg(algorithm),
150 159 
                            ignore.strand = ignore.strand, ...)
151 160 
           })
152 161
Browse code

The findOverlaps() generic got a new 'algorithm' argument in IRanges 2.1.10 (commit 96627). So add it to all "findOverlaps" methods defined in bsseq.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@96631 bc3139a8-67e5-0310-9ffc-ced21a209358

hpages@fhcrc.org authored on 08/11/2014 02:53:46
Showing 1 changed files
R/hasGRanges.R
History View file @ 1d865e3
... ... 
@@ -121,10 +121,13 @@ setMethod("findOverlaps",
121 121 
           signature(query = "hasGRanges", subject = "GenomicRanges"),
122 122 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
123 123 
                     type = c("any", "start", "end", "within", "equal"),
124 
-                    select = c("all", "first"), ignore.strand = FALSE, ...) {
124 
+                    select = c("all", "first"),
125 
+                    algorithm = c("intervaltree", "nclist"),
126 
+                    ignore.strand = FALSE, ...) {
125 127 
               findOverlaps(query = granges(query), subject = subject,
126 128 
                            maxgap = maxgap, minoverlap = minoverlap,
127 129 
                            type = match.arg(type), select = match.arg(select),
130 
+                           algorithm = match.arg(algorithm),
128 131 
                            ignore.strand = ignore.strand, ...)
129 132 
           })
130 133
... ... 
@@ -132,10 +135,13 @@ setMethod("findOverlaps",
132 135 
           signature(query = "hasGRanges", subject = "hasGRanges"),
133 136 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
134 137 
                     type = c("any", "start", "end", "within", "equal"),
135 
-                    select = c("all", "first"), ignore.strand = FALSE, ...) {
138 
+                    select = c("all", "first"),
139 
+                    algorithm = c("intervaltree", "nclist"),
140 
+                    ignore.strand = FALSE, ...) {
136 141 
               findOverlaps(query = granges(query), subject = granges(subject),
137 142 
                            maxgap = maxgap, minoverlap = minoverlap,
138 143 
                            type = match.arg(type), select = match.arg(select),
144 
+                           algorithm = match.arg(algorithm),
139 145 
                            ignore.strand = ignore.strand, ...)
140 146 
           })
141 147
... ... 
@@ -143,10 +149,13 @@ setMethod("findOverlaps",
143 149 
           signature(query = "GenomicRanges", subject = "hasGRanges"),
144 150 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
145 151 
                     type = c("any", "start", "end", "within", "equal"),
146 
-                    select = c("all", "first"), ignore.strand = FALSE, ...) {
152 
+                    select = c("all", "first"),
153 
+                    algorithm = c("intervaltree", "nclist"),
154 
+                    ignore.strand = FALSE, ...) {
147 155 
               findOverlaps(query = query, subject = granges(subject),
148 156 
                            maxgap = maxgap, minoverlap = minoverlap,
149 157 
                            type = match.arg(type), select = match.arg(select),
158 
+                           algorithm = match.arg(algorithm),
150 159 
                            ignore.strand = ignore.strand, ...)
151 160 
           })
152 161
Browse code

Version bump; various fixes to address issues reported by R CMD check, including documentation, use of :::, and deprecation of seqselect

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@81150 bc3139a8-67e5-0310-9ffc-ced21a209358

Kasper D. Hansen authored on 04/10/2013 15:23:24
Showing 1 changed files
R/hasGRanges.R
History View file @ 8e5853a
... ... 
@@ -86,10 +86,10 @@ setMethod("subsetByOverlaps",
86 86 
           function(query, subject, maxgap = 0L, minoverlap = 1L,
87 87 
                    type = c("any", "start", "end", "within", "equal"),
88 88 
                    ignore.strand = FALSE, ...) {
89 
-              ov <- findOverlaps_mclapply(query = granges(query), subject = subject,
90 
-                                          maxgap = maxgap, minoverlap = minoverlap,
91 
-                                          type = match.arg(type), select = "first",
92 
-                                          ignore.strand = ignore.strand, ... )
89 
+              ov <- findOverlaps(query = granges(query), subject = subject,
90 
+                                 maxgap = maxgap, minoverlap = minoverlap,
91 
+                                 type = match.arg(type), select = "first",
92 
+                                 ignore.strand = ignore.strand, ... )
93 93 
               query[!is.na(ov)]
94 94 
           })
95 95
... ... 
@@ -98,10 +98,10 @@ setMethod("subsetByOverlaps",
98 98 
           function(query, subject, maxgap = 0L, minoverlap = 1L,
99 99 
                    type = c("any", "start", "end", "within", "equal"),
100 100 
                    ignore.strand = FALSE, ...) {
101 
-              ov <- findOverlaps_mclapply(query = granges(query), subject = granges(subject),
102 
-                                          maxgap = maxgap, minoverlap = minoverlap,
103 
-                                          type = match.arg(type), select = "first",
104 
-                                          ignore.strand = ignore.strand, ... )
101 
+              ov <- findOverlaps(query = granges(query), subject = granges(subject),
102 
+                                 maxgap = maxgap, minoverlap = minoverlap,
103 
+                                 type = match.arg(type), select = "first",
104 
+                                 ignore.strand = ignore.strand, ... )
105 105 
               query[!is.na(ov)]
106 106 
           })
107 107
... ... 
@@ -110,10 +110,10 @@ setMethod("subsetByOverlaps",
110 110 
           function(query, subject, maxgap = 0L, minoverlap = 1L,
111 111 
                    type = c("any", "start", "end", "within", "equal"),
112 112 
                    ignore.strand = FALSE, ...) {
113 
-              ov <- findOverlaps_mclapply(query = query, subject = granges(subject),
114 
-                                          maxgap = maxgap, minoverlap = minoverlap,
115 
-                                          type = match.arg(type), select = "first",
116 
-                                          ignore.strand = ignore.strand, ... )
113 
+              ov <- findOverlaps(query = query, subject = granges(subject),
114 
+                                 maxgap = maxgap, minoverlap = minoverlap,
115 
+                                 type = match.arg(type), select = "first",
116 
+                                 ignore.strand = ignore.strand, ... )
117 117 
               query[!is.na(ov)]
118 118 
           })
119 119
... ... 
@@ -122,10 +122,10 @@ setMethod("findOverlaps",
122 122 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
123 123 
                     type = c("any", "start", "end", "within", "equal"),
124 124 
                     select = c("all", "first"), ignore.strand = FALSE, ...) {
125 
-              findOverlaps_mclapply(query = granges(query), subject = subject,
126 
-                                    maxgap = maxgap, minoverlap = minoverlap,
127 
-                                    type = match.arg(type), select = match.arg(select),
128 
-                                    ignore.strand = ignore.strand, ...)
125 
+              findOverlaps(query = granges(query), subject = subject,
126 
+                           maxgap = maxgap, minoverlap = minoverlap,
127 
+                           type = match.arg(type), select = match.arg(select),
128 
+                           ignore.strand = ignore.strand, ...)
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           })
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 setMethod("findOverlaps",
... ... 
@@ -133,10 +133,10 @@ setMethod("findOverlaps",
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           function (query, subject, maxgap = 0L, minoverlap = 1L,
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                     type = c("any", "start", "end", "within", "equal"),
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                     select = c("all", "first"), ignore.strand = FALSE, ...) {
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-              findOverlaps_mclapply(query = granges(query), subject = granges(subject),
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-                                    maxgap = maxgap, minoverlap = minoverlap,
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-                                    type = match.arg(type), select = match.arg(select),
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-                                    ignore.strand = ignore.strand, ...)
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+              findOverlaps(query = granges(query), subject = granges(subject),
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+                           maxgap = maxgap, minoverlap = minoverlap,
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+                           type = match.arg(type), select = match.arg(select),
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+                           ignore.strand = ignore.strand, ...)
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           })
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 setMethod("findOverlaps",
... ... 
@@ -144,10 +144,10 @@ setMethod("findOverlaps",
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           function (query, subject, maxgap = 0L, minoverlap = 1L,
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                     type = c("any", "start", "end", "within", "equal"),
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                     select = c("all", "first"), ignore.strand = FALSE, ...) {
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-              findOverlaps_mclapply(query = query, subject = granges(subject),
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-                                    maxgap = maxgap, minoverlap = minoverlap,
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-                                    type = match.arg(type), select = match.arg(select),
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-                                    ignore.strand = ignore.strand, ...)
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+              findOverlaps(query = query, subject = granges(subject),
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+                           maxgap = maxgap, minoverlap = minoverlap,
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+                           type = match.arg(type), select = match.arg(select),
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+                           ignore.strand = ignore.strand, ...)
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           })
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 setMethod("[", "hasGRanges", function(x, i, ...) {
Browse code

Version bump; various fixes to address issues reported by R CMD check, including documentation, use of :::, and deprecation of seqselect

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@81150 bc3139a8-67e5-0310-9ffc-ced21a209358

khansen authored on 04/10/2013 15:23:24
Showing 1 changed files
R/hasGRanges.R
History View file @ 1824727
... ... 
@@ -86,10 +86,10 @@ setMethod("subsetByOverlaps",
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           function(query, subject, maxgap = 0L, minoverlap = 1L,
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                    type = c("any", "start", "end", "within", "equal"),
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                    ignore.strand = FALSE, ...) {
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-              ov <- findOverlaps_mclapply(query = granges(query), subject = subject,
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-                                          maxgap = maxgap, minoverlap = minoverlap,
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-                                          type = match.arg(type), select = "first",
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-                                          ignore.strand = ignore.strand, ... )
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+              ov <- findOverlaps(query = granges(query), subject = subject,
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+                                 maxgap = maxgap, minoverlap = minoverlap,
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+                                 type = match.arg(type), select = "first",
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+                                 ignore.strand = ignore.strand, ... )
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               query[!is.na(ov)]
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           })
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... ... 
@@ -98,10 +98,10 @@ setMethod("subsetByOverlaps",
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           function(query, subject, maxgap = 0L, minoverlap = 1L,
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                    type = c("any", "start", "end", "within", "equal"),
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                    ignore.strand = FALSE, ...) {
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-              ov <- findOverlaps_mclapply(query = granges(query), subject = granges(subject),
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-                                          maxgap = maxgap, minoverlap = minoverlap,
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-                                          type = match.arg(type), select = "first",
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-                                          ignore.strand = ignore.strand, ... )
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+              ov <- findOverlaps(query = granges(query), subject = granges(subject),
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+                                 maxgap = maxgap, minoverlap = minoverlap,
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+                                 type = match.arg(type), select = "first",
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+                                 ignore.strand = ignore.strand, ... )
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               query[!is.na(ov)]
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           })
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... ... 
@@ -110,10 +110,10 @@ setMethod("subsetByOverlaps",
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           function(query, subject, maxgap = 0L, minoverlap = 1L,
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                    type = c("any", "start", "end", "within", "equal"),
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                    ignore.strand = FALSE, ...) {
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-              ov <- findOverlaps_mclapply(query = query, subject = granges(subject),
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-                                          maxgap = maxgap, minoverlap = minoverlap,
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-                                          type = match.arg(type), select = "first",
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-                                          ignore.strand = ignore.strand, ... )
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+              ov <- findOverlaps(query = query, subject = granges(subject),
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+                                 maxgap = maxgap, minoverlap = minoverlap,
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+                                 type = match.arg(type), select = "first",
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+                                 ignore.strand = ignore.strand, ... )
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               query[!is.na(ov)]
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           })
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... ... 
@@ -122,10 +122,10 @@ setMethod("findOverlaps",
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           function (query, subject, maxgap = 0L, minoverlap = 1L,
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                     type = c("any", "start", "end", "within", "equal"),
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                     select = c("all", "first"), ignore.strand = FALSE, ...) {
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-              findOverlaps_mclapply(query = granges(query), subject = subject,
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-                                    maxgap = maxgap, minoverlap = minoverlap,
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-                                    type = match.arg(type), select = match.arg(select),
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-                                    ignore.strand = ignore.strand, ...)
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+              findOverlaps(query = granges(query), subject = subject,
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+                           maxgap = maxgap, minoverlap = minoverlap,
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+                           type = match.arg(type), select = match.arg(select),
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+                           ignore.strand = ignore.strand, ...)
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           })
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 setMethod("findOverlaps",
... ... 
@@ -133,10 +133,10 @@ setMethod("findOverlaps",
133 133 
           function (query, subject, maxgap = 0L, minoverlap = 1L,
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                     type = c("any", "start", "end", "within", "equal"),
135 135 
                     select = c("all", "first"), ignore.strand = FALSE, ...) {
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-              findOverlaps_mclapply(query = granges(query), subject = granges(subject),
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-                                    maxgap = maxgap, minoverlap = minoverlap,
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-                                    type = match.arg(type), select = match.arg(select),
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-                                    ignore.strand = ignore.strand, ...)
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+              findOverlaps(query = granges(query), subject = granges(subject),
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+                           maxgap = maxgap, minoverlap = minoverlap,
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+                           type = match.arg(type), select = match.arg(select),
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+                           ignore.strand = ignore.strand, ...)
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           })
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 setMethod("findOverlaps",
... ... 
@@ -144,10 +144,10 @@ setMethod("findOverlaps",
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           function (query, subject, maxgap = 0L, minoverlap = 1L,
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                     type = c("any", "start", "end", "within", "equal"),
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                     select = c("all", "first"), ignore.strand = FALSE, ...) {
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-              findOverlaps_mclapply(query = query, subject = granges(subject),
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-                                    maxgap = maxgap, minoverlap = minoverlap,
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-                                    type = match.arg(type), select = match.arg(select),
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-                                    ignore.strand = ignore.strand, ...)
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+              findOverlaps(query = query, subject = granges(subject),
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+                           maxgap = maxgap, minoverlap = minoverlap,
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+                           type = match.arg(type), select = match.arg(select),
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+                           ignore.strand = ignore.strand, ...)
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           })
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153