forked from tidyomics/plyinteractions
-
Notifications
You must be signed in to change notification settings - Fork 0
/
NAMESPACE
285 lines (284 loc) · 8.28 KB
/
NAMESPACE
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
# Generated by roxygen2: do not edit by hand
S3method(anchor,AnchoredPinnedGInteractions)
S3method(anchor_3p,AnchoredPinnedGInteractions)
S3method(anchor_3p,PinnedGInteractions)
S3method(anchor_5p,AnchoredPinnedGInteractions)
S3method(anchor_5p,PinnedGInteractions)
S3method(anchor_center,AnchoredPinnedGInteractions)
S3method(anchor_center,PinnedGInteractions)
S3method(anchor_end,AnchoredPinnedGInteractions)
S3method(anchor_end,PinnedGInteractions)
S3method(anchor_start,AnchoredPinnedGInteractions)
S3method(anchor_start,PinnedGInteractions)
S3method(arrange,GInteractions)
S3method(as_ginteractions,data.frame)
S3method(as_ginteractions,default)
S3method(count,GInteractions)
S3method(count,GroupedGInteractions)
S3method(count_overlaps,GInteractions)
S3method(count_overlaps,PinnedGInteractions)
S3method(count_overlaps_directed,GInteractions)
S3method(count_overlaps_directed,PinnedGInteractions)
S3method(filter,GInteractions)
S3method(filter_by_non_overlaps,GInteractions)
S3method(filter_by_non_overlaps,PinnedGInteractions)
S3method(filter_by_overlaps,GInteractions)
S3method(filter_by_overlaps,PinnedGInteractions)
S3method(find_overlaps,GInteractions)
S3method(find_overlaps,PinnedGInteractions)
S3method(find_overlaps_directed,GInteractions)
S3method(find_overlaps_directed,PinnedGInteractions)
S3method(flank_downstream,PinnedGInteractions)
S3method(flank_downstream,Ranges)
S3method(flank_left,PinnedGInteractions)
S3method(flank_left,Ranges)
S3method(flank_right,PinnedGInteractions)
S3method(flank_right,Ranges)
S3method(flank_upstream,PinnedGInteractions)
S3method(flank_upstream,Ranges)
S3method(group_by,DelegatingGInteractions)
S3method(group_by,GInteractions)
S3method(group_by,GroupedGInteractions)
S3method(group_data,GroupedGInteractions)
S3method(group_indices,GroupedGInteractions)
S3method(group_keys,GroupedGInteractions)
S3method(group_size,GroupedGInteractions)
S3method(group_vars,GInteractions)
S3method(group_vars,GroupedGInteractions)
S3method(groups,GroupedGInteractions)
S3method(join_overlap_left,GInteractions)
S3method(join_overlap_left,PinnedGInteractions)
S3method(join_overlap_left_directed,GInteractions)
S3method(join_overlap_left_directed,PinnedGInteractions)
S3method(mutate,GInteractions)
S3method(n_groups,GroupedGInteractions)
S3method(rename,GInteractions)
S3method(select,GInteractions)
S3method(shift_downstream,PinnedGInteractions)
S3method(shift_downstream,Ranges)
S3method(shift_left,PinnedGInteractions)
S3method(shift_left,Ranges)
S3method(shift_right,PinnedGInteractions)
S3method(shift_right,Ranges)
S3method(shift_upstream,PinnedGInteractions)
S3method(shift_upstream,Ranges)
S3method(slice,GInteractions)
S3method(stretch,AnchoredPinnedGInteractions)
S3method(stretch,PinnedGInteractions)
S3method(summarise,GroupedGInteractions)
S3method(summarize,GroupedGInteractions)
S3method(tally,GroupedGInteractions)
S3method(tbl_vars,GInteractions)
S3method(unanchor,AnchoredPinnedGInteractions)
S3method(ungroup,GroupedGInteractions)
export(add_pairdist)
export(anchor)
export(anchor_3p)
export(anchor_5p)
export(anchor_center)
export(anchor_end)
export(anchor_start)
export(anchors1)
export(anchors2)
export(annotate)
export(annotate_directed)
export(arrange)
export(as_ginteractions)
export(count)
export(count_overlaps)
export(count_overlaps_directed)
export(end1)
export(end2)
export(filter)
export(filter_by_non_overlaps)
export(filter_by_overlaps)
export(find_overlaps)
export(find_overlaps_directed)
export(flank_downstream)
export(flank_left)
export(flank_right)
export(flank_upstream)
export(group_by)
export(group_data)
export(group_indices)
export(group_keys)
export(group_rows)
export(group_size)
export(group_vars)
export(groups)
export(join_overlap_left)
export(join_overlap_left_directed)
export(mutate)
export(n_groups)
export(pair_granges)
export(pin)
export(pin_anchors1)
export(pin_anchors2)
export(pin_by)
export(pin_first)
export(pin_second)
export(pinned_anchors)
export(ranges1)
export(ranges2)
export(rename)
export(replace_anchors)
export(select)
export(seqnames1)
export(seqnames2)
export(shift_downstream)
export(shift_left)
export(shift_right)
export(shift_upstream)
export(slice)
export(start1)
export(start2)
export(strand1)
export(strand2)
export(stretch)
export(summarise)
export(summarize)
export(tally)
export(unanchor)
export(ungroup)
export(unpin)
export(width1)
export(width2)
export(write_bedpe)
export(write_pairs)
exportMethods("$")
exportMethods(anchors1)
exportMethods(anchors2)
exportMethods(annotate)
exportMethods(annotate_directed)
exportMethods(end1)
exportMethods(end2)
exportMethods(pin)
exportMethods(pinned_anchors)
exportMethods(ranges1)
exportMethods(ranges2)
exportMethods(replace_anchors)
exportMethods(seqnames1)
exportMethods(seqnames2)
exportMethods(start1)
exportMethods(start2)
exportMethods(strand1)
exportMethods(strand2)
exportMethods(unpin)
exportMethods(width1)
exportMethods(width2)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,width)
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,granges)
importFrom(IRanges,IRanges)
importFrom(IRanges,ranges)
importFrom(IRanges,subsetByOverlaps)
importFrom(InteractionSet,GInteractions)
importFrom(InteractionSet,anchors)
importFrom(InteractionSet,countOverlaps)
importFrom(InteractionSet,findOverlaps)
importFrom(InteractionSet,regions)
importFrom(S4Vectors,"first<-")
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,"second<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,as.env)
importFrom(S4Vectors,cbind)
importFrom(S4Vectors,decode)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,queryLength)
importFrom(S4Vectors,rbind)
importFrom(S4Vectors,showAsCell)
importFrom(S4Vectors,subjectHits)
importFrom(S4Vectors,subjectLength)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,count)
importFrom(dplyr,desc)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,group_data)
importFrom(dplyr,group_indices)
importFrom(dplyr,group_keys)
importFrom(dplyr,group_rows)
importFrom(dplyr,group_size)
importFrom(dplyr,group_vars)
importFrom(dplyr,groups)
importFrom(dplyr,mutate)
importFrom(dplyr,n_groups)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(dplyr,summarise)
importFrom(dplyr,summarize)
importFrom(dplyr,tally)
importFrom(dplyr,tbl_vars)
importFrom(dplyr,ungroup)
importFrom(methods,as)
importFrom(methods,getGeneric)
importFrom(methods,getGenerics)
importFrom(methods,initialize)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,prototype)
importFrom(methods,representation)
importFrom(methods,selectMethod)
importFrom(methods,setMethod)
importFrom(methods,show)
importFrom(methods,validObject)
importFrom(plyranges,anchor)
importFrom(plyranges,anchor_3p)
importFrom(plyranges,anchor_5p)
importFrom(plyranges,anchor_center)
importFrom(plyranges,anchor_end)
importFrom(plyranges,anchor_start)
importFrom(plyranges,as_granges)
importFrom(plyranges,count_overlaps)
importFrom(plyranges,count_overlaps_directed)
importFrom(plyranges,filter_by_non_overlaps)
importFrom(plyranges,filter_by_overlaps)
importFrom(plyranges,find_overlaps)
importFrom(plyranges,find_overlaps_directed)
importFrom(plyranges,flank_downstream)
importFrom(plyranges,flank_left)
importFrom(plyranges,flank_right)
importFrom(plyranges,flank_upstream)
importFrom(plyranges,join_overlap_left)
importFrom(plyranges,join_overlap_left_directed)
importFrom(plyranges,set_width)
importFrom(plyranges,shift_downstream)
importFrom(plyranges,shift_left)
importFrom(plyranges,shift_right)
importFrom(plyranges,shift_upstream)
importFrom(plyranges,stretch)
importFrom(plyranges,unanchor)
importFrom(rlang,"!!!")
importFrom(rlang,`:=`)
importFrom(rlang,enquo)
importFrom(rlang,enquos)
importFrom(rlang,eval_tidy)
importFrom(rlang,expr)
importFrom(rlang,inform)
importFrom(rlang,is_call)
importFrom(rlang,local_options)
importFrom(rlang,quo)
importFrom(rlang,quo_get_expr)
importFrom(rlang,quo_is_null)
importFrom(rlang,quo_name)
importFrom(rlang,quos)
importFrom(rlang,set_names)
importFrom(rlang,sym)
importFrom(rlang,syms)
importFrom(rlang,warn)
importFrom(tibble,as_tibble)
importFrom(tidyselect,eval_rename)
importFrom(tidyselect,eval_select)
importFrom(utils,.DollarNames)
importFrom(utils,capture.output)