This file is indexed.

/usr/lib/R/site-library/S4Vectors/help/AnIndex is in r-bioc-s4vectors 0.16.0-1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  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
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
!,Rle-method	Rle-utils
!=,ANY,Vector-method	Vector-comparison
!=,Vector,ANY-method	Vector-comparison
!=,Vector,Vector-method	Vector-comparison
$,List-method	List-class
$<-,List-method	List-class
%in%,ANY,Vector-method	Vector-comparison
%in%,Rle,ANY-method	Rle-class
%in%,Vector,ANY-method	Vector-comparison
%in%,Vector,Vector-method	Vector-comparison
.Call2	S4Vectors-internals
<,ANY,Vector-method	Vector-comparison
<,Vector,ANY-method	Vector-comparison
<,Vector,Vector-method	Vector-comparison
<=,ANY,Vector-method	Vector-comparison
<=,Vector,ANY-method	Vector-comparison
<=,Vector,Vector-method	Vector-comparison
==,ANY,Vector-method	Vector-comparison
==,Vector,ANY-method	Vector-comparison
==,Vector,Vector-method	Vector-comparison
>,ANY,Vector-method	Vector-comparison
>,Vector,ANY-method	Vector-comparison
>,Vector,Vector-method	Vector-comparison
>=,ANY,Vector-method	Vector-comparison
>=,Vector,ANY-method	Vector-comparison
>=,Vector,Vector-method	Vector-comparison
active	FilterRules-class
active,FilterRules-method	FilterRules-class
active<-	FilterRules-class
active<-,FilterRules-method	FilterRules-class
aggregate	aggregate-methods
aggregate,data.frame-method	aggregate-methods
aggregate,List-method	aggregate-methods
aggregate,matrix-method	aggregate-methods
aggregate,Rle-method	aggregate-methods
aggregate,ts-method	aggregate-methods
aggregate,Vector-method	aggregate-methods
aggregate-methods	aggregate-methods
aggregate.Vector	aggregate-methods
Annotated	Annotated-class
Annotated-class	Annotated-class
anyDuplicated,NSBS-method	subsetting-utils
anyDuplicated,RangeNSBS-method	subsetting-utils
anyDuplicated.NSBS	subsetting-utils
anyNA,Vector-method	Vector-class
append,FilterRules,FilterRules-method	FilterRules-class
append,Rle,vector-method	Rle-class
append,vector,Rle-method	Rle-class
append,Vector,Vector-method	Vector-class
as.character,LLint-method	LLint-class
as.character,Vector-method	Vector-class
as.character.LLint	LLint-class
as.complex,Vector-method	Vector-class
as.data.frame,DataFrame-method	DataFrame-class
as.data.frame,DataTable-method	DataTable-class
as.data.frame,List-method	List-class
as.data.frame,Pairs-method	Pairs-class
as.data.frame,Rle-method	Rle-class
as.data.frame,Vector-method	Vector-class
as.data.frame.DataTable	DataTable-class
as.data.frame.Vector	Vector-class
as.double,Vector-method	Vector-class
as.env	DataTable-class
as.env,DataTable-method	DataTable-class
as.env,NULL-method	DataTable-class
as.env,Vector-method	Vector-class
as.factor,Rle-method	Rle-class
as.integer,LLint-method	LLint-class
as.integer,NativeNSBS-method	subsetting-utils
as.integer,RangeNSBS-method	subsetting-utils
as.integer,Vector-method	Vector-class
as.integer.LLint	LLint-class
as.list,List-method	List-class
as.list,Rle-method	Rle-class
as.list,SimpleList-method	SimpleList-class
as.list,Vector-method	Vector-class
as.list.Vector	Vector-class
as.LLint	LLint-class
as.logical,LLint-method	LLint-class
as.logical,Vector-method	Vector-class
as.logical.LLint	LLint-class
as.matrix,DataFrame-method	DataFrame-class
as.matrix,Hits-method	Hits-class
as.matrix,HitsList-method	HitsList-class
as.matrix,Vector-method	Vector-class
as.matrix.Vector	Vector-class
as.numeric,LLint-method	LLint-class
as.numeric,Vector-method	Vector-class
as.numeric.LLint	LLint-class
as.raw,Vector-method	Vector-class
as.table,Hits-method	Hits-class
as.table,HitsList-method	HitsList-class
as.vector,Rle-method	Rle-class
as.vector.Rle	Rle-class
breakTies	Hits-class
by,DataTable-method	DataTable-class
c,FilterRules-method	FilterRules-class
c,Hits-method	Hits-class
c,LLint-method	LLint-class
c,Pairs-method	Pairs-class
c,Rle-method	Rle-class
c,SimpleList-method	SimpleList-class
cbind,DataFrame-method	DataFrame-class
cbind,DataTable-method	DataTable-class
cbind,FilterMatrix-method	FilterMatrix-class
cbind,List-method	List-utils
character_OR_NULL	S4Vectors-internals
character_OR_NULL-class	S4Vectors-internals
chartr,ANY,ANY,Rle-method	Rle-utils
class:character_OR_NULL	S4Vectors-internals
class:DataFrame	DataFrame-class
class:DataTable	DataTable-class
class:DataTable_OR_NULL	Vector-class
class:expression_OR_function	FilterRules-class
class:FilterRules	FilterRules-class
class:Hits	Hits-class
class:HitsList	HitsList-class
class:List	List-class
class:LLint	LLint-class
class:NSBS	subsetting-utils
class:Pairs	Pairs-class
class:Rle	Rle-class
class:SelfHits	Hits-class
class:SelfHitsList	HitsList-class
class:SimpleList	SimpleList-class
class:SortedByQueryHits	Hits-class
class:SortedByQueryHitsList	HitsList-class
class:SortedByQuerySelfHits	Hits-class
class:SortedByQuerySelfHitsList	HitsList-class
class:Vector	Vector-class
class:vector_OR_factor	S4Vectors-internals
classNameForDisplay	show-utils
classNameForDisplay,ANY-method	show-utils
classNameForDisplay,AsIs-method	show-utils
classNameForDisplay,Hits-method	Hits-class
classNameForDisplay,SelfHits-method	Hits-class
classNameForDisplay,SimpleList-method	SimpleList-class
coerce,ANY,AsIs-method	DataFrame-class
coerce,ANY,DataFrame-method	DataFrame-class
coerce,ANY,List-method	List-class
coerce,ANY,SimpleList-method	SimpleList-class
coerce,ANY,vector-method	S4Vectors-internals
coerce,AsIs,DataFrame-method	DataFrame-class
coerce,character,LLint-method	LLint-class
coerce,character,Rle-method	Rle-class
coerce,complex,Rle-method	Rle-class
coerce,data.frame,DataFrame-method	DataFrame-class
coerce,data.table,DataFrame-method	DataFrame-class
coerce,DataFrame,data.frame-method	DataFrame-class
coerce,factor,Rle-method	Rle-class
coerce,function,FilterClosure-method	FilterRules-class
coerce,Hits,SortedByQueryHits-method	Hits-class
coerce,integer,DataFrame-method	DataFrame-class
coerce,integer,List-method	List-class
coerce,integer,LLint-method	LLint-class
coerce,integer,Rle-method	Rle-class
coerce,List,data.frame-method	List-class
coerce,list,DataFrame-method	DataFrame-class
coerce,List,list-method	List-class
coerce,list,List-method	SimpleList-class
coerce,logical,LLint-method	LLint-class
coerce,logical,Rle-method	Rle-class
coerce,matrix,DataFrame-method	DataFrame-class
coerce,NULL,DataFrame-method	DataFrame-class
coerce,numeric,LLint-method	LLint-class
coerce,numeric,Rle-method	Rle-class
coerce,Pairs,DataFrame-method	Pairs-class
coerce,raw,Rle-method	Rle-class
coerce,Rle,character-method	Rle-class
coerce,Rle,complex-method	Rle-class
coerce,Rle,data.frame-method	Rle-class
coerce,Rle,factor-method	Rle-class
coerce,Rle,integer-method	Rle-class
coerce,Rle,list-method	Rle-class
coerce,Rle,logical-method	Rle-class
coerce,Rle,numeric-method	Rle-class
coerce,Rle,raw-method	Rle-class
coerce,Rle,vector-method	Rle-class
coerce,SimpleList,DataFrame-method	DataFrame-class
coerce,standardGeneric,FilterClosure-method	FilterRules-class
coerce,table,DataFrame-method	DataFrame-class
coerce,Vector,character-method	Vector-class
coerce,Vector,complex-method	Vector-class
coerce,Vector,data.frame-method	Vector-class
coerce,Vector,DataFrame-method	DataFrame-class
coerce,vector,DataFrame-method	DataFrame-class
coerce,Vector,double-method	Vector-class
coerce,Vector,factor-method	Vector-class
coerce,Vector,integer-method	Vector-class
coerce,Vector,logical-method	Vector-class
coerce,Vector,numeric-method	Vector-class
coerce,Vector,raw-method	Vector-class
coerce,vector,Rle-method	Rle-class
coerce,Vector,vector-method	Vector-class
coerce,xtabs,DataFrame-method	DataFrame-class
colnames,DataFrame-method	DataFrame-class
colnames<-,DataFrame-method	DataFrame-class
complete.cases,DataTable-method	DataTable-class
Complex,Rle-method	Rle-utils
cor,Rle,Rle-method	Rle-utils
countLnodeHits	Hits-class
countLnodeHits,Hits-method	Hits-class
countMatches	Vector-comparison
countMatches,ANY,ANY-method	Vector-comparison
countQueryHits	Hits-class
countRnodeHits	Hits-class
countRnodeHits,Hits-method	Hits-class
countSubjectHits	Hits-class
cov,Rle,Rle-method	Rle-utils
DataFrame	DataFrame-class
DataFrame-class	DataFrame-class
DataTable	DataTable-class
DataTable-class	DataTable-class
DataTable_OR_NULL	Vector-class
DataTable_OR_NULL-class	Vector-class
decode	Rle-class
decode,ANY-method	Rle-class
decode,Rle-method	Rle-class
diff,Rle-method	Rle-utils
diff.Rle	Rle-utils
dim,DataTable-method	DataTable-class
dimnames,DataTable-method	DataTable-class
dimnames<-,DataTable-method	DataTable-class
droplevels,List-method	List-utils
droplevels,Rle-method	Rle-utils
droplevels.List	List-utils
droplevels.Rle	Rle-utils
duplicated,DataTable-method	DataTable-class
duplicated,Rle-method	Rle-class
duplicated,Vector-method	Vector-comparison
duplicated.DataTable	DataTable-class
duplicated.Vector	Vector-comparison
duplicatedIntegerPairs	S4Vectors-internals
duplicatedIntegerQuads	S4Vectors-internals
elementMetadata	Vector-class
elementMetadata,Vector-method	Vector-class
elementMetadata<-	Vector-class
elementMetadata<-,Vector-method	Vector-class
elementNROWS	List-class
elementNROWS,ANY-method	List-class
elementNROWS,List-method	List-class
elementType	List-class
elementType,List-method	List-class
elementType,vector-method	List-class
end,Rle-method	Rle-class
endoapply	List-utils
endoapply,data.frame-method	List-utils
endoapply,List-method	List-utils
endoapply,list-method	List-utils
endoapply,SimpleList-method	SimpleList-class
eval,FilterRules,ANY-method	FilterRules-class
evalSeparately	FilterRules-class
evalSeparately,FilterRules-method	FilterRules-class
expand	expand-methods
expand,DataFrame-method	expand-methods
expand,Vector-method	expand-methods
expand.grid	Vector-class
expand.grid,Vector-method	Vector-class
expression_OR_function	FilterRules-class
expression_OR_function-class	FilterRules-class
extractROWS	subsetting-utils
extractROWS,ANY,ANY-method	subsetting-utils
extractROWS,classNameForDisplay,ANY-method	Hits-class
extractROWS,Rle,ANY-method	Rle-class
extractROWS,Rle,RangeNSBS-method	Rle-class
extractROWS,vector_OR_factor,RangeNSBS-method	subsetting-utils
Filter,List-method	List-utils
FilterMatrix	FilterMatrix-class
FilterMatrix-class	FilterMatrix-class
FilterRules	FilterRules-class
filterRules	FilterMatrix-class
filterRules,FilterMatrix-method	FilterMatrix-class
FilterRules-class	FilterRules-class
Find,List-method	List-utils
findMatches	Vector-comparison
findMatches,ANY,ANY-method	Vector-comparison
findMatches,ANY,missing-method	Vector-comparison
findRun	Rle-class
findRun,Rle-method	Rle-class
first	Pairs-class
first,Pairs-method	Pairs-class
first<-	Pairs-class
first<-,Pairs-method	Pairs-class
fold	S4Vectors-internals
from	Hits-class
from,Hits-method	Hits-class
getListElement	subsetting-utils
get_showHeadLines	S4Vectors-internals
get_showTailLines	S4Vectors-internals
gsub,ANY,ANY,Rle-method	Rle-utils
head	Vector-class
head,Vector-method	Vector-class
head.DataTable	DataTable-class
head.Vector	Vector-class
Hits	Hits-class
Hits-class	Hits-class
Hits-comparison	Hits-comparison
Hits-setops	Hits-setops
HitsList	HitsList-class
HitsList-class	HitsList-class
intersect,ANY,Rle-method	Rle-class
intersect,Rle,ANY-method	Rle-class
intersect,Rle,Rle-method	Rle-class
intersect,Vector,Vector-method	Vector-setops
intersect.Vector	Vector-setops
IQR,Rle-method	Rle-utils
is.LLint	LLint-class
is.na,DataTable-method	DataTable-class
is.na,LLint-method	LLint-class
is.na,Rle-method	Rle-class
is.na,Vector-method	Vector-class
is.unsorted,Rle-method	Rle-class
isConstant	isSorted
isConstant,array-method	isSorted
isConstant,integer-method	isSorted
isConstant,numeric-method	isSorted
isEmpty	List-class
isEmpty,ANY-method	List-class
isEmpty,List-method	List-class
isRedundantHit	Hits-class
isSelfHit	Hits-class
isSingleInteger	S4Vectors-internals
isSingleNumber	S4Vectors-internals
isSingleNumberOrNA	S4Vectors-internals
isSingleString	S4Vectors-internals
isSingleStringOrNA	S4Vectors-internals
isSorted	isSorted
isSorted,ANY-method	isSorted
isStrictlySorted	isSorted
isStrictlySorted,ANY-method	isSorted
isStrictlySorted,NSBS-method	subsetting-utils
isStrictlySorted,RangeNSBS-method	subsetting-utils
isTRUEorFALSE	S4Vectors-internals
lapply,List-method	List-utils
lapply,SimpleList-method	SimpleList-class
length,LLint-method	LLint-class
length,NSBS-method	subsetting-utils
length,Pairs-method	Pairs-class
length,RangeNSBS-method	subsetting-utils
length,Rle-method	Rle-class
length,SimpleList-method	SimpleList-class
length,Vector-method	Vector-class
lengths,Vector-method	Vector-class
levels,Rle-method	Rle-utils
levels.Rle	Rle-utils
levels<-,Rle-method	Rle-utils
List	List-class
List-class	List-class
List-utils	List-utils
LLint	LLint-class
LLint-class	LLint-class
mad,Rle-method	Rle-utils
mad.Rle	Rle-utils
Map,List-method	List-utils
match,Hits,Hits-method	Hits-comparison
match,Pairs,Pairs-method	Pairs-class
match,Rle,ANY-method	Rle-class
matchIntegerPairs	S4Vectors-internals
matchIntegerQuads	S4Vectors-internals
Math,Rle-method	Rle-utils
Math2,Rle-method	Rle-utils
mcols	Vector-class
mcols,Vector-method	Vector-class
mcols<-	Vector-class
mcols<-,Vector-method	Vector-class
mean,Rle-method	Rle-utils
mean.Rle	Rle-utils
median,Rle-method	Rle-utils
median.Rle	Rle-utils
mendoapply	List-utils
mendoapply,data.frame-method	List-utils
mendoapply,List-method	List-utils
mendoapply,list-method	List-utils
mendoapply,SimpleList-method	SimpleList-class
merge	Vector-merge
merge,data.frame,DataTable-method	DataTable-class
merge,DataTable,data.frame-method	DataTable-class
merge,DataTable,DataTable-method	DataTable-class
merge,Vector,Vector-method	Vector-merge
metadata	Annotated-class
metadata,Annotated-method	Annotated-class
metadata<-	Annotated-class
metadata<-,Annotated-method	Annotated-class
na.exclude,DataTable-method	DataTable-class
na.omit,DataTable-method	DataTable-class
names,Pairs-method	Pairs-class
names,SimpleList-method	SimpleList-class
names<-,Pairs-method	Pairs-class
names<-,SimpleList-method	SimpleList-class
NA_LLint_	LLint-class
nchar,Rle-method	Rle-utils
ncol,DataFrame-method	DataFrame-class
NCOL,DataTable-method	DataTable-class
new2	S4Vectors-internals
nLnode	Hits-class
nLnode,Hits-method	Hits-class
nnode	Hits-class
nnode,SelfHits-method	Hits-class
normalizeDoubleBracketSubscript	subsetting-utils
normalizeSingleBracketReplacementValue	subsetting-utils
normalizeSingleBracketReplacementValue,ANY-method	subsetting-utils
normalizeSingleBracketSubscript	subsetting-utils
nRnode	Hits-class
nRnode,Hits-method	Hits-class
nrow,DataFrame-method	DataFrame-class
NROW,DataTable-method	DataTable-class
NROW,Vector-method	Vector-class
nrun	Rle-class
nrun,Rle-method	Rle-class
NSBS	subsetting-utils
NSBS,array-method	subsetting-utils
NSBS,character-method	subsetting-utils
NSBS,factor-method	subsetting-utils
NSBS,logical-method	subsetting-utils
NSBS,missing-method	subsetting-utils
NSBS,NSBS-method	subsetting-utils
NSBS,NULL-method	subsetting-utils
NSBS,numeric-method	subsetting-utils
NSBS-class	subsetting-utils
Ops,LLint,LLint-method	LLint-class
Ops,LLint,numeric-method	LLint-class
Ops,numeric,LLint-method	LLint-class
Ops,Rle,Rle-method	Rle-utils
Ops,Rle,vector-method	Rle-utils
Ops,vector,Rle-method	Rle-utils
order,Hits-method	Hits-comparison
orderIntegerPairs	S4Vectors-internals
orderIntegerQuads	S4Vectors-internals
Pairs	Pairs-class
Pairs-class	Pairs-class
parallelSlotNames,Hits-method	Hits-class
parallelSlotNames,Pairs-method	Pairs-class
parallelVectorNames	Vector-class
parallelVectorNames,ANY-method	Vector-class
parallelVectorNames,List-method	List-class
params	FilterRules-class
params,FilterClosure-method	FilterRules-class
paste,Rle-method	Rle-utils
pc	List-utils
pcompare	Vector-comparison
pcompare,Hits,Hits-method	Hits-comparison
pmax,Rle-method	Rle-utils
pmax.int,Rle-method	Rle-utils
pmin,Rle-method	Rle-utils
pmin.int,Rle-method	Rle-utils
Position,List-method	List-utils
printAtomicVectorInAGrid	S4Vectors-internals
quantile,Rle-method	Rle-utils
quantile.Rle	Rle-utils
queryHits	Hits-class
queryHits,HitsList-method	HitsList-class
queryLength	Hits-class
rank,Vector-method	Vector-comparison
rbind,DataFrame-method	DataFrame-class
rbind,DataTable-method	DataTable-class
rbind,FilterMatrix-method	FilterMatrix-class
rbind,List-method	List-utils
recycleArg	S4Vectors-internals
recycleCharacterArg	S4Vectors-internals
recycleIntegerArg	S4Vectors-internals
recycleLogicalArg	S4Vectors-internals
recycleNumericArg	S4Vectors-internals
Reduce,List-method	List-utils
relistToClass	List-class
relistToClass,ANY-method	List-class
relistToClass,Hits-method	HitsList-class
relistToClass,SortedByQueryHits-method	HitsList-class
remapHits	Hits-class
rename	Vector-class
rename,Vector-method	Vector-class
rename,vector-method	Vector-class
rep,Rle-method	Rle-class
rep.int,Rle-method	Rle-class
replaceROWS	subsetting-utils
replaceROWS,ANY-method	subsetting-utils
replaceROWS,Vector-method	Vector-class
rev,Rle-method	Rle-class
rev.Rle	Rle-class
revElements	List-utils
revElements,List-method	List-utils
revElements,list-method	List-utils
Rle	Rle-class
Rle,ANY-method	Rle-class
Rle,Rle-method	Rle-class
Rle-class	Rle-class
Rle-runstat	Rle-runstat
Rle-utils	Rle-utils
ROWNAMES	DataTable-class
ROWNAMES,ANY-method	DataTable-class
rownames,DataFrame-method	DataFrame-class
ROWNAMES,DataTable-method	DataTable-class
ROWNAMES,Vector-method	Vector-class
rownames<-,DataFrame-method	DataFrame-class
runLength	Rle-class
runLength,Rle-method	Rle-class
runLength<-	Rle-class
runLength<-,Rle-method	Rle-class
runmean	Rle-runstat
runmean,Rle-method	Rle-runstat
runmed,Rle-method	Rle-runstat
runq	Rle-runstat
runq,Rle-method	Rle-runstat
runsum	Rle-runstat
runsum,Rle-method	Rle-runstat
runValue	Rle-class
runValue,Rle-method	Rle-class
runValue<-	Rle-class
runValue<-,Rle-method	Rle-class
runwtsum	Rle-runstat
runwtsum,Rle-method	Rle-runstat
safeExplode	character-utils
sapply,List-method	List-utils
sd,Rle-method	Rle-utils
second	Pairs-class
second,Pairs-method	Pairs-class
second<-	Pairs-class
second<-,Pairs-method	Pairs-class
SelfHits	Hits-class
SelfHits-class	Hits-class
SelfHitsList	HitsList-class
SelfHitsList-class	HitsList-class
selfmatch	Vector-comparison
selfmatch,ANY-method	Vector-comparison
selfmatch,factor-method	Vector-comparison
selfmatchIntegerPairs	S4Vectors-internals
selfmatchIntegerQuads	S4Vectors-internals
setdiff,ANY,Rle-method	Rle-class
setdiff,Rle,ANY-method	Rle-class
setdiff,Rle,Rle-method	Rle-class
setdiff,Vector,Vector-method	Vector-setops
setdiff.Vector	Vector-setops
setequal,Vector,Vector-method	Vector-setops
setequal.Vector	Vector-setops
setListElement	subsetting-utils
setMethods	S4Vectors-internals
setValidity2	S4Vectors-internals
shiftApply	shiftApply-methods
shiftApply,Vector,Vector-method	shiftApply-methods
shiftApply,vector,vector-method	shiftApply-methods
shiftApply-methods	shiftApply-methods
show,DataTable-method	DataTable-class
show,FilterClosure-method	FilterRules-class
show,FilterMatrix-method	FilterMatrix-class
show,Hits-method	Hits-class
show,List-method	List-class
show,LLint-method	LLint-class
show,Pairs-method	Pairs-class
show,RangeNSBS-method	subsetting-utils
show,Rle-method	Rle-class
show-utils	show-utils
showAsCell	show-utils
showAsCell,ANY-method	show-utils
showAsCell,AsIs-method	show-utils
showAsCell,Date-method	show-utils
showAsCell,LLint-method	LLint-class
showAsCell,POSIXt-method	show-utils
showAsCell,Rle-method	Rle-class
SimpleList	SimpleList-class
SimpleList-class	SimpleList-class
smoothEnds,Rle-method	Rle-runstat
sort,Rle-method	Rle-class
sort,Vector-method	Vector-comparison
sort.Vector	Vector-comparison
SortedByQueryHits	Hits-class
SortedByQueryHits-class	Hits-class
SortedByQueryHitsList	HitsList-class
SortedByQueryHitsList-class	HitsList-class
SortedByQuerySelfHits	Hits-class
SortedByQuerySelfHits-class	Hits-class
SortedByQuerySelfHitsList	HitsList-class
SortedByQuerySelfHitsList-class	HitsList-class
space	HitsList-class
space,HitsList-method	HitsList-class
split	split-methods
split,ANY,Vector-method	split-methods
split,list,Vector-method	split-methods
split,Vector,ANY-method	split-methods
split,Vector,Vector-method	split-methods
split-methods	split-methods
start,Rle-method	Rle-class
strsplitAsListOfIntegerVectors	character-utils
sub,ANY,ANY,Rle-method	Rle-utils
subjectHits	Hits-class
subjectHits,HitsList-method	HitsList-class
subjectLength	Hits-class
subset,DataTable-method	DataTable-class
subsetByFilter	FilterRules-class
subsetByFilter,ANY,FilterRules-method	FilterRules-class
subsetting-utils	subsetting-utils
substr,Rle-method	Rle-utils
substring,Rle-method	Rle-utils
summary,FilterMatrix-method	FilterMatrix-class
summary,FilterRules-method	FilterRules-class
Summary,LLint-method	LLint-class
Summary,Rle-method	Rle-utils
summary,Rle-method	Rle-utils
summary.Rle	Rle-utils
svn.time	character-utils
t,Hits-method	Hits-class
t,HitsList-method	HitsList-class
table,Rle-method	Rle-class
table,Vector-method	Vector-comparison
tabulate,Rle-method	Rle-class
tail	Vector-class
tail,Vector-method	Vector-class
tail.DataTable	DataTable-class
tail.Vector	Vector-class
to	Hits-class
to,Hits-method	Hits-class
tolower,Rle-method	Rle-utils
toupper,Rle-method	Rle-utils
transform,DataTable-method	DataTable-class
transform.DataTable	DataTable-class
union,ANY,Rle-method	Rle-class
union,Hits,Hits-method	Hits-setops
union,Rle,ANY-method	Rle-class
union,Rle,Rle-method	Rle-class
union,Vector,Vector-method	Vector-setops
union.Vector	Vector-setops
unique,DataTable-method	DataTable-class
unique,Rle-method	Rle-class
unique,Vector-method	Vector-comparison
unique.DataTable	DataTable-class
unique.Vector	Vector-comparison
unlist,List-method	List-class
unstrsplit	character-utils
unstrsplit,character-method	character-utils
unstrsplit,list-method	character-utils
updateObject,Hits-method	Hits-class
values	Vector-class
values,Vector-method	Vector-class
values<-	Vector-class
values<-,Vector-method	Vector-class
var,Rle,missing-method	Rle-utils
var,Rle,Rle-method	Rle-utils
Vector	Vector-class
Vector-class	Vector-class
Vector-comparison	Vector-comparison
Vector-merge	Vector-merge
Vector-setops	Vector-setops
vector_OR_factor	S4Vectors-internals
vector_OR_factor-class	S4Vectors-internals
which,Rle-method	Rle-utils
which.max,Rle-method	Rle-utils
width,Rle-method	Rle-class
window	Vector-class
window,Vector-method	Vector-class
window.Vector	Vector-class
within,List-method	List-utils
wmsg	S4Vectors-internals
xtabs,DataTable-method	DataTable-class
zipdown	zip-methods
zipdown,ANY-method	zip-methods
zipdown,List-method	zip-methods
zipup	zip-methods
zipup,ANY,ANY-method	zip-methods
zipup,Pairs,missing-method	Pairs-class
[,DataFrame-method	DataFrame-class
[,FilterMatrix-method	FilterMatrix-class
[,FilterRules-method	FilterRules-class
[,List-method	List-class
[,Rle-method	Rle-class
[,Vector-method	Vector-class
[<-,DataFrame-method	DataFrame-class
[<-,List-method	List-class
[<-,Rle-method	Rle-class
[<-,Vector-method	Vector-class
[[,DataFrame-method	DataFrame-class
[[,List-method	List-class
[[<-,DataFrame-method	DataFrame-class
[[<-,FilterRules-method	FilterRules-class
[[<-,List-method	List-class