1. bsseq
  2. Commit 659aee2ab5a3eb073a31ba3a98e7d0aaab2095a6
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 4 changed files
DESCRIPTION
History View file @ 659aee2
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.25.0
2 
+Version: 1.25.1
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
... ... 
@@ -14,7 +14,7 @@ Depends:
14 14 
     GenomicRanges (>= 1.33.6),
15 15 
     SummarizedExperiment (>= 1.17.4)
16 16 
 Imports:
17 
-    IRanges (>= 2.21.6),
17 
+    IRanges (>= 2.23.5),
18 18 
     GenomeInfoDb,
19 19 
     scales,
20 20 
     stats,
NAMESPACE
History View file @ 659aee2
... ... 
@@ -72,7 +72,7 @@ exportMethods("[", "show",
72 72 
               "dim", "nrow", "ncol",
73 73 
               "sampleNames", "sampleNames<-",
74 74 
               "pData", "pData<-",
75 
-              "findOverlaps", "subsetByOverlaps",
75 
+              "findOverlaps", "overlapsAny", "subsetByOverlaps",
76 76 
               "combine", "updateObject")
77 77
78 78 
 export("BSseq", "getMeth", "getCoverage", "getBSseq", "getStats",
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
man/hasGRanges-class.Rd
History View file @ 659aee2
... ... 
@@ -1,32 +1,37 @@
1 1 
 \name{hasGRanges-class}
2 2 
 \Rdversion{1.1}
3 3 
 \docType{class}
4 
+\alias{class:hasGRanges}
4 5 
 \alias{hasGRanges-class}
5 
-\alias{[,hasGRanges-method}
6 
-\alias{[,hasGRanges,ANY,ANY,ANY-method}
7 
-\alias{end,hasGRanges-method}
8 
-\alias{end<-,hasGRanges-method}
9 
-\alias{granges,hasGRanges-method}
10 
-\alias{length,hasGRanges-method}
11 
-\alias{seqlengths,hasGRanges-method}
12 
-\alias{seqlengths<-,hasGRanges-method}
13 
-\alias{seqlevels,hasGRanges-method}
14 
-\alias{seqlevels<-,hasGRanges-method}
6 
+\alias{hasGRanges}
15 7 
 \alias{seqnames,hasGRanges-method}
16 8 
 \alias{seqnames<-,hasGRanges-method}
9 
+\alias{seqlevels,hasGRanges-method}
10 
+\alias{seqlevels<-,hasGRanges-method}
11 
+\alias{seqlengths,hasGRanges-method}
12 
+\alias{seqlengths<-,hasGRanges-method}
13 
+\alias{granges,hasGRanges-method}
17 14 
 \alias{start,hasGRanges-method}
18 15 
 \alias{start<-,hasGRanges-method}
16 
+\alias{end,hasGRanges-method}
17 
+\alias{end<-,hasGRanges-method}
18 
+\alias{width,hasGRanges-method}
19 
+\alias{width<-,hasGRanges-method}
19 20 
 \alias{strand,hasGRanges-method}
20 21 
 \alias{strand<-,hasGRanges-method}
21 22 
 \alias{strand<-,hasGRanges,ANY-method}
22 
-%\alias{subsetByOverlaps,GenomicRanges,hasGRanges-method}
23 
-%\alias{subsetByOverlaps,hasGRanges,GenomicRanges-method}
24 
-%\alias{subsetByOverlaps,hasGRanges,hasGRanges-method}
25 
-\alias{findOverlaps,GenomicRanges,hasGRanges-method}
23 
+\alias{length,hasGRanges-method}
24 
+\alias{[,hasGRanges-method}
25 
+\alias{[,hasGRanges,ANY,ANY,ANY-method}
26 26 
 \alias{findOverlaps,hasGRanges,GenomicRanges-method}
27 
+\alias{findOverlaps,GenomicRanges,hasGRanges-method}
27 28 
 \alias{findOverlaps,hasGRanges,hasGRanges-method}
28 
-\alias{width,hasGRanges-method}
29 
-\alias{width<-,hasGRanges-method}
29 
+\alias{overlapsAny,hasGRanges,GenomicRanges-method}
30 
+\alias{overlapsAny,GenomicRanges,hasGRanges-method}
31 
+\alias{overlapsAny,hasGRanges,hasGRanges-method}
32 
+\alias{subsetByOverlaps,hasGRanges,GenomicRanges-method}
33 
+\alias{subsetByOverlaps,GenomicRanges,hasGRanges-method}
34 
+\alias{subsetByOverlaps,hasGRanges,hasGRanges-method}
30 35
31 36 
 \title{Class hasGRanges}
32 37 
 \description{