Global functions | |
---|---|
!,Rle-method | Man page |
!=,ANY,Vector-method | Man page |
!=,Vector,ANY-method | Man page |
!=,Vector,Vector-method | Man page |
$,List-method | Man page |
$<-,List-method | Man page |
%in%,ANY,Vector-method | Man page |
%in%,Rle,ANY-method | Man page |
%in%,Vector,ANY-method | Man page |
%in%,Vector,Vector-method | Man page |
&,FilterRules,FilterRules-method | Man page |
.AEbufs_free | Source code |
.AEbufs_use_malloc | Source code |
.Call2 | Man page Source code |
.Factor_as | Source code |
.Hits_summary | Source code |
.NSBS.character_OR_factor | Source code |
.NSBS.numeric | Source code |
.ReduceDefault | Source code |
.VectorAsDataFrame | Source code |
.Vector_shiftApply | Source code |
.Vector_summary | Source code |
.add_missing_columns | Source code |
.adjust_elt_lengths | Source code |
.adjust_value_length | Source code |
.aggregate.List | Source code |
.aggregate.Rle | Source code |
.aggregate.Vector | Source code |
.allEqualS4 | Source code |
.anyDuplicated.Vector | Source code |
.append_list_element | Source code |
.as.data.frame.DataFrame | Source code |
.as.data.frame.List | Source code |
.as.data.frame.Rle | Source code |
.as.list.List | Source code |
.as.list.Rle | Source code |
.as.list.SimpleList | Source code |
.atomic_sameAsPreviousROW | Source code |
.bindROWS_DataFrame_objects | Source code |
.bind_cols_along_their_ROWS | Source code |
.check_that_Hits_objects_are_concatenable | Source code |
.collapse_list_of_equal_vectors | Source code |
.compatible_Hits | Source code |
.compute_table | Source code |
.concatenate_Factor_objects | Source code |
.concatenate_Hits_objects | Source code |
.concatenate_LLint_objects | Source code |
.concatenate_Rle_objects | Source code |
.concatenate_two_Factor_objects | Source code |
.countMatches.default | Source code |
.count_Lnode_hits | Source code |
.count_Rnode_hits | Source code |
.defaultAsDataFrame | Source code |
.default_bindROWS | Source code |
.default_showAsCell | Source code |
.diff.Rle | Source code |
.droplevels.List | Source code |
.droplevels.Rle | Source code |
.duplicated.List | Source code |
.duplicated.Rle | Source code |
.duplicated.Vector | Source code |
.ellipsize | Source code |
.encode_as_Factor | Source code |
.expand | Source code |
.expandCols | Source code |
.fast_lsubset_List_by_List | Source code |
.fast_subset_List_by_LL | Source code |
.fast_subset_List_by_NL | Source code |
.fast_subset_List_by_RL | Source code |
.fill_short_columns | Source code |
.findAllMatchesInSmallTable | Source code |
.format_mismatch_message | Source code |
.from_HitsList_SortedByQueryHitsList | Source code |
.from_Hits_to_SelfHits | Source code |
.from_Hits_to_SortedByQueryHits | Source code |
.from_Hits_to_naked_character_matrix_for_display | Source code |
.from_LLint_to_character | Source code |
.from_LLint_to_integer | Source code |
.from_LLint_to_logical | Source code |
.from_LLint_to_numeric | Source code |
.from_Pairs_to_naked_character_matrix_for_display | Source code |
.from_SortedByQueryHitsList_to_HitsList | Source code |
.from_character_to_LLint | Source code |
.from_integer_to_LLint | Source code |
.from_logical_to_LLint | Source code |
.from_numeric_to_LLint | Source code |
.get_showLines | Source code |
.is_valid_NL_subscript | Source code |
.islistfactor | Source code |
.list.names | Source code Source code |
.make_colmaps | Source code |
.make_colnames | Source code |
.make_endoapply_ans | Source code |
.make_group_and_group_name | Source code |
.make_mcols | Source code |
.make_rownames | Source code |
.make_unlisted_names | Source code |
.matchIntegerPairs_hash | Source code |
.matchIntegerPairs_quick | Source code |
.matchIntegerQuads_hash | Source code |
.matchIntegerQuads_quick | Source code |
.match_name | Source code |
.mean.Rle | Source code |
.mergeByHits | Source code |
.merge_Vector_objects | Source code |
.merge_mcols | Source code |
.merge_naked_objects | Source code |
.nasafe_compare | Source code |
.new_Factor | Source code |
.new_Hits | Source code |
.normBindArgs | Source code |
.normargIntegerOrFactor | Source code |
.normargMethod | Source code |
.normarg_new.nnode | Source code |
.normarg_nodes.remapping | Source code |
.normarg_range_start | Source code |
.normarg_vector_length | Source code |
.numeric_sameAsPreviousROW | Source code |
.onLoad | Source code |
.onUnload | Source code |
.op1_apply | Source code |
.op2_apply | Source code |
.padToAlign | Source code |
.pasteTwoRles | Source code |
.psummary.Rle | Source code |
.qualifyByName | Source code |
.relistToClass_DataFrame | Source code |
.remove_list_element | Source code |
.renameVector | Source code |
.rep_times_Rle | Source code |
.replace_list_element | Source code |
.same_levels | Source code |
.selectListClassName | Source code |
.select_fast_path | Source code |
.selfmatchIntegerPairs_hash | Source code |
.selfmatchIntegerPairs_quick | Source code |
.selfmatchIntegerQuads_hash | Source code |
.selfmatchIntegerQuads_quick | Source code |
.set_names_on_unfactor_ans | Source code |
.show_DataFrame | Source code |
.show_Factor | Source code |
.show_Hits | Source code |
.show_LLint | Source code |
.show_TransposedDataFrame | Source code |
.sort_List | Source code |
.sort_Vector | Source code |
.subassign_columns | Source code |
.subscript_error | Source code |
.subset_TransposedDataFrame | Source code |
.sumprodRle | Source code |
.test | Source code |
.two_factor_comparison | Source code |
.unique.List | Source code |
.unique.Rle | Source code |
.unique.SimpleList | Source code |
.unique.Vector | Source code |
.unlist_LL_subscript | Source code |
.unlist_NL_subscript | Source code |
.unlist_RL_subscript | Source code |
.valid.DataFrame | Source code |
.valid.DataFrame.dim | Source code |
.valid.DataFrame.names | Source code |
.valid.DataFrame.rownames | Source code |
.valid.FilterRules | Source code |
.valid.FilterRules.active | Source code |
.valid.FilterRules.rules | Source code |
.valid.Hits | Source code |
.valid.Hits.from_or_to | Source code |
.valid.Hits.nnode | Source code |
.valid.SelfHits | Source code |
.valid.SimpleList | Source code |
.valid.SimpleList.listData | Source code |
.valid.SortedByQueryHits | Source code |
.valid_Rle | Source code |
.validate_Factor | Source code |
.validate_RectangularData | Source code |
.validate_Vector | Source code |
.validate_Vector_length | Source code |
.validate_Vector_mcols | Source code |
.validate_Vector_names | Source code |
.validate_Vector_parallel_slots | Source code |
.wrap_in_length_one_list_like_object | Source code |
<,ANY,Vector-method | Man page |
<,Vector,ANY-method | Man page |
<,Vector,Vector-method | Man page |
<=,ANY,Vector-method | Man page |
<=,DataFrame,DataFrame-method | Man page |
<=,Vector,ANY-method | Man page |
<=,Vector,Vector-method | Man page |
==,ANY,Vector-method | Man page |
==,DataFrame,DataFrame-method | Man page |
==,Vector,ANY-method | Man page |
==,Vector,Vector-method | Man page |
>,ANY,Vector-method | Man page |
>,Vector,ANY-method | Man page |
>,Vector,Vector-method | Man page |
>=,ANY,Vector-method | Man page |
>=,Vector,ANY-method | Man page |
>=,Vector,Vector-method | Man page |
Annotated | Man page |
Annotated-class | Man page |
Complex,Rle-method | Man page |
DFrame | Man page |
DFrame-class | Man page |
DataFrame | Man page Source code |
DataFrame-class | Man page |
DataFrame-utils | Man page |
DataFrame_OR_NULL | Man page |
DataFrame_OR_NULL-class | Man page |
Factor | Man page Source code |
Factor-class | Man page |
FactorToClass | Man page |
FactorToClass,vector_OR_Vector-method | Man page |
Filter,List-method | Man page |
FilterMatrix | Man page |
FilterMatrix-class | Man page |
FilterRules | Man page Source code |
FilterRules-class | Man page |
FilterRules.parseRule | Source code |
Find,List-method | Man page |
H_recycle | Source code |
Has | Source code |
Hits | Man page Source code |
Hits-class | Man page |
Hits-comparison | Man page |
Hits-setops | Man page |
HitsList | Man page Source code |
HitsList-class | Man page |
IQR,Rle-method | Man page |
LLint | Man page Source code |
LLint-class | Man page |
List | Man page Source code |
List-class | Man page |
List-utils | Man page |
Map,List-method | Man page |
Math,Rle-method | Man page |
Math2,Rle-method | Man page |
ModelFrame | Source code |
NA_LLint_ | Man page |
NSBS | Man page |
NSBS,NSBS-method | Man page |
NSBS,NULL-method | Man page |
NSBS,Rle-method | Man page |
NSBS,array-method | Man page |
NSBS,character-method | Man page |
NSBS,factor-method | Man page |
NSBS,logical-method | Man page |
NSBS,missing-method | Man page |
NSBS,numeric-method | Man page |
NSBS-class | Man page |
NativeNSBS | Source code |
Ops,LLint,LLint-method | Man page |
Ops,LLint,numeric-method | Man page |
Ops,Rle,Rle-method | Man page |
Ops,Rle,vector-method | Man page |
Ops,numeric,LLint-method | Man page |
Ops,vector,Rle-method | Man page |
Pairs | Man page Source code |
Pairs-class | Man page |
Position,List-method | Man page |
ROWNAMES | Man page |
ROWNAMES,ANY-method | Man page |
ROWNAMES,RectangularData-method | Man page |
RangeNSBS | Source code |
RectangularData | Man page |
RectangularData-class | Man page |
Reduce,List-method | Man page |
Rle | Man page |
Rle,ANY-method | Man page |
Rle,Rle-method | Man page |
Rle-class | Man page |
Rle-runstat | Man page |
Rle-utils | Man page |
SelfHits | Man page Source code |
SelfHits-class | Man page |
SelfHitsList | Man page |
SelfHitsList-class | Man page |
SimpleList | Man page Source code |
SimpleList-class | Man page |
SortedByQueryHits | Man page |
SortedByQueryHits-class | Man page |
SortedByQueryHitsList | Man page |
SortedByQueryHitsList-class | Man page |
SortedByQuerySelfHits | Man page |
SortedByQuerySelfHits-class | Man page |
SortedByQuerySelfHitsList | Man page |
SortedByQuerySelfHitsList-class | Man page |
Summary,LLint-method | Man page |
Summary,Rle-method | Man page |
TransposedDataFrame | Man page |
TransposedDataFrame-class | Man page |
VH_recycle | Source code |
V_recycle | Source code |
Vector | Man page |
Vector-class | Man page |
Vector-comparison | Man page |
Vector-merge | Man page |
Vector-setops | Man page |
Vector_window | Source code |
[ | Man page |
[,DataFrame-method | Man page |
[,FilterMatrix-method | Man page |
[,FilterRules-method | Man page |
[,List-method | Man page |
[,Rle-method | Man page |
[,TransposedDataFrame-method | Man page |
[,Vector-method | Man page |
[<-,DataFrame-method | Man page |
[<-,List-method | Man page |
[<-,Rle,ANY-method | Man page |
[<-,Vector-method | Man page |
[[,DataFrame-method | Man page |
[[,List-method | Man page |
[[<-,DataFrame-method | Man page |
[[<-,FilterRules-method | Man page |
[[<-,List-method | Man page |
active | Man page |
active,FilterRules-method | Man page |
active<- | Man page |
active<-,FilterRules-method | Man page |
addSelfRef | Source code |
aggregate | Man page |
aggregate,List-method | Man page |
aggregate,Rle-method | Man page |
aggregate,Vector-method | Man page |
aggregate,data.frame-method | Man page |
aggregate,matrix-method | Man page |
aggregate,ts-method | Man page |
aggregate-methods | Man page |
aggregate.Vector | Man page Source code |
aggregateWithDots | Source code |
allEqualS4 | Source code |
anyDuplicated,NSBS-method | Man page |
anyDuplicated,RangeNSBS-method | Man page |
anyDuplicated,Rle-method | Man page |
anyDuplicated,RleNSBS-method | Man page |
anyDuplicated,Vector-method | Man page |
anyDuplicated.NSBS | Man page Source code |
anyDuplicated.Rle | Man page Source code |
anyDuplicated.Vector | Man page Source code |
anyMissing | Source code |
anyMissingOrOutside | Source code |
anyNA,Rle-method | Man page |
anyNA,Vector-method | Man page |
append | Man page |
append,Rle,vector-method | Man page |
append,Vector,Vector-method | Man page |
append,vector,Rle-method | Man page |
as.LLint | Man page Source code |
as.character,Factor-method | Man page |
as.character,LLint-method | Man page |
as.character,Vector-method | Man page |
as.character.LLint | Man page Source code |
as.complex,Vector-method | Man page |
as.data.frame,DataFrame-method | Man page |
as.data.frame,Hits-method | Man page |
as.data.frame,List-method | Man page |
as.data.frame,Pairs-method | Man page |
as.data.frame,Rle-method | Man page |
as.data.frame,Vector-method | Man page |
as.data.frame.Hits | Man page Source code |
as.data.frame.Vector | Man page Source code |
as.double,Vector-method | Man page |
as.env | Man page |
as.env,NULL-method | Man page |
as.env,SimpleList-method | Man page |
as.env,Vector-method | Man page |
as.factor,Factor-method | Man page |
as.factor,Rle-method | Man page |
as.integer,Factor-method | Man page |
as.integer,LLint-method | Man page |
as.integer,NativeNSBS-method | Man page |
as.integer,RangeNSBS-method | Man page |
as.integer,RleNSBS-method | Man page |
as.integer,Vector-method | Man page |
as.integer.LLint | Man page Source code |
as.list,List-method | Man page |
as.list,Rle-method | Man page |
as.list,SimpleList-method | Man page |
as.list,TransposedDataFrame-method | Man page |
as.list,Vector-method | Man page |
as.list.Vector | Man page Source code |
as.logical,LLint-method | Man page |
as.logical,Vector-method | Man page |
as.logical.LLint | Man page Source code |
as.matrix,DataFrame-method | Man page |
as.matrix,Hits-method | Man page |
as.matrix,HitsList-method | Man page |
as.matrix,TransposedDataFrame-method | Man page |
as.matrix,Vector-method | Man page |
as.matrix.Vector | Man page Source code |
as.numeric,LLint-method | Man page |
as.numeric,Vector-method | Man page |
as.numeric.LLint | Man page Source code |
as.raw,Vector-method | Man page |
as.table,Hits-method | Man page |
as.table,HitsList-method | Man page |
as.vector,Rle-method | Man page |
as.vector.Rle | Man page Source code |
asFactorOrFactorRle | Source code |
atomic | Man page |
atomic-class | Man page |
bindCOLS | Man page |
bindCOLS,TransposedDataFrame-method | Man page |
bindROWS | Man page |
bindROWS,ANY-method | Man page |
bindROWS,DataFrame-method | Man page |
bindROWS,Factor-method | Man page |
bindROWS,Hits-method | Man page |
bindROWS,LLint-method | Man page |
bindROWS,NULL-method | Man page |
bindROWS,Rle-method | Man page |
bindROWS,TransposedDataFrame-method | Man page |
bindROWS,Vector-method | Man page |
breakTies | Man page Source code |
c | Man page |
c,DataFrame-method | Man page |
c,LLint-method | Man page |
c,Vector-method | Man page |
canonical_replace_as | Source code |
canonical_replace_as_2 | Source code |
capitalize | Source code |
cbind,DataFrame-method | Man page |
cbind,FilterMatrix-method | Man page |
cbind,List-method | Man page |
cbind,RectangularData-method | Man page |
cbind.DataFrame | Man page Source code |
cbind.RectangularData | Man page Source code |
cbind_mcols_for_display | Man page Source code |
character_OR_NULL | Man page |
character_OR_NULL-class | Man page |
chartr,ANY,ANY,Rle-method | Man page |
class:DFrame | Man page |
class:DataFrame | Man page |
class:DataFrame_OR_NULL | Man page |
class:Factor | Man page |
class:FilterRules | Man page |
class:Hits | Man page |
class:HitsList | Man page |
class:LLint | Man page |
class:List | Man page |
class:NSBS | Man page |
class:Pairs | Man page |
class:RectangularData | Man page |
class:Rle | Man page |
class:SelfHits | Man page |
class:SelfHitsList | Man page |
class:SimpleList | Man page |
class:SortedByQueryHits | Man page |
class:SortedByQueryHitsList | Man page |
class:SortedByQuerySelfHits | Man page |
class:SortedByQuerySelfHitsList | Man page |
class:TransposedDataFrame | Man page |
class:Vector | Man page |
class:atomic | Man page |
class:character_OR_NULL | Man page |
class:expression_OR_function | Man page |
class:integer_OR_LLint | Man page |
class:list_OR_List | Man page |
class:vector_OR_Vector | Man page |
class:vector_OR_factor | Man page |
classNameForDisplay | Man page |
classNameForDisplay,ANY-method | Man page |
classNameForDisplay,AsIs-method | Man page |
classNameForDisplay,DFrame-method | Man page |
classNameForDisplay,SimpleList-method | Man page |
classNameForDisplay,SortedByQueryHits-method | Man page |
classNamespace | Source code |
coerce,ANY,AsIs-method | Man page |
coerce,ANY,DFrame-method | Man page |
coerce,ANY,DataFrame-method | Man page |
coerce,ANY,FilterRules-method | Man page |
coerce,ANY,List-method | Man page |
coerce,ANY,Rle-method | Man page |
coerce,ANY,SimpleList-method | Man page |
coerce,ANY,vector-method | Man page |
coerce,AsIs,DFrame-method | Man page |
coerce,DFrame,DataFrame-method | Man page |
coerce,DataFrame,TransposedDataFrame-method | Man page |
coerce,Hits,DFrame-method | Man page |
coerce,Hits,SelfHits-method | Man page |
coerce,Hits,SortedByQueryHits-method | Man page |
coerce,Hits,SortedByQuerySelfHits-method | Man page |
coerce,HitsList,SortedByQueryHitsList-method | Man page |
coerce,List,list-method | Man page |
coerce,NULL,DFrame-method | Man page |
coerce,Pairs,DFrame-method | Man page |
coerce,Rle,character-method | Man page |
coerce,Rle,complex-method | Man page |
coerce,Rle,factor-method | Man page |
coerce,Rle,integer-method | Man page |
coerce,Rle,list-method | Man page |
coerce,Rle,logical-method | Man page |
coerce,Rle,numeric-method | Man page |
coerce,Rle,raw-method | Man page |
coerce,Rle,vector-method | Man page |
coerce,SelfHits,SortedByQuerySelfHits-method | Man page |
coerce,SimpleList,DFrame-method | Man page |
coerce,SimpleList,DataFrame-method | Man page |
coerce,SimpleList,FilterRules-method | Man page |
coerce,SortedByQueryHits,SortedByQuerySelfHits-method | Man page |
coerce,SortedByQueryHitsList,HitsList-method | Man page |
coerce,TransposedDataFrame,DataFrame-method | Man page |
coerce,Vector,DFrame-method | Man page |
coerce,Vector,character-method | Man page |
coerce,Vector,complex-method | Man page |
coerce,Vector,data.frame-method | Man page |
coerce,Vector,double-method | Man page |
coerce,Vector,factor-method | Man page |
coerce,Vector,integer-method | Man page |
coerce,Vector,logical-method | Man page |
coerce,Vector,numeric-method | Man page |
coerce,Vector,raw-method | Man page |
coerce,Vector,vector-method | Man page |
coerce,character,LLint-method | Man page |
coerce,data.frame,DFrame-method | Man page |
coerce,data.table,DFrame-method | Man page |
coerce,factor,Factor-method | Man page |
coerce,function,FilterClosure-method | Man page |
coerce,integer,LLint-method | Man page |
coerce,integer,List-method | Man page |
coerce,list,DFrame-method | Man page |
coerce,list,List-method | Man page |
coerce,list,TransposedDataFrame-method | Man page |
coerce,list_OR_List,Pairs-method | Man page |
coerce,logical,LLint-method | Man page |
coerce,numeric,LLint-method | Man page |
coerce,standardGeneric,FilterClosure-method | Man page |
coerce,table,DFrame-method | Man page |
coerce,vector_OR_Vector,Factor-method | Man page |
coerce,xtabs,DFrame-method | Man page |
coerceToSimpleList | Source code |
coercerToClass | Source code |
colnames,DataFrame-method | Man page |
colnames<-,DataFrame-method | Man page |
complete.cases,DataFrame-method | Man page |
compress_listData | Source code |
concatenate_Vector_objects | Source code |
coolcat | Man page Source code |
cor,Rle,Rle-method | Man page |
countLnodeHits | Man page |
countLnodeHits,Hits-method | Man page |
countMatches | Man page |
countMatches,ANY,ANY-method | Man page |
countQueryHits | Man page Source code |
countRnodeHits | Man page |
countRnodeHits,Hits-method | Man page |
countSubjectHits | Man page Source code |
cov,Rle,Rle-method | Man page |
debugValidity | Source code |
decode | Man page |
decode,ANY-method | Man page |
decode,Rle-method | Man page |
decodeRle | Source code |
defaultIndices | Source code |
default_extractROWS | Source code |
default_mergeROWS | Source code |
default_replaceROWS | Source code |
delete_NULLs | Source code |
diff,Rle-method | Man page |
diff.Rle | Man page Source code |
diff.Vector | Source code |
diffWithInitialZero | Source code |
diffWithLast | Source code |
dim,DataFrame-method | Man page |
dim,TransposedDataFrame-method | Man page |
dimnames,DataFrame-method | Man page |
dimnames,TransposedDataFrame-method | Man page |
dimnames<-,DataFrame-method | Man page |
dimnames<-,TransposedDataFrame-method | Man page |
disableValidity | Source code |
drop_AsIs | Source code |
droplevels,List-method | Man page |
droplevels,Rle-method | Man page |
droplevels.DataFrame | Source code |
droplevels.List | Man page Source code |
droplevels.Rle | Man page Source code |
duplicated,DataFrame-method | Man page |
duplicated,Rle-method | Man page |
duplicated,Vector-method | Man page |
duplicated.DataFrame | Man page Source code |
duplicated.Vector | Man page Source code |
duplicatedIntegerPairs | Man page Source code |
duplicatedIntegerQuads | Man page Source code |
elementMetadata | Man page |
elementMetadata,Vector-method | Man page |
elementMetadata<- | Man page |
elementMetadata<-,Vector-method | Man page |
elementNROWS | Man page |
elementNROWS,ANY-method | Man page |
elementNROWS,List-method | Man page |
elementType | Man page |
elementType,List-method | Man page |
elementType,vector-method | Man page |
end,Rle-method | Man page |
endoapply | Man page Source code |
ensureMcols | Source code |
errorIfWarning | Source code |
eval,FilterRules,ANY-method | Man page |
evalArg | Source code |
evalSeparately | Man page |
evalSeparately,FilterRules-method | Man page |
evalqForSelect | Source code |
evalqForSubset | Source code |
expand | Man page |
expand,DataFrame-method | Man page |
expand,Vector-method | Man page |
expand.grid | Man page |
expand.grid,Vector-method | Man page |
expandByColumnSet | Source code |
explodeIntBits | Source code |
expression_OR_function | Man page |
expression_OR_function-class | Man page |
extraArgsAsList | Source code |
extractCOLS | Man page |
extractCOLS,TransposedDataFrame-method | Man page |
extractROWS | Man page |
extractROWS,ANY,ANY-method | Man page |
extractROWS,Rle,ANY-method | Man page |
extractROWS,Rle,NSBS-method | Man page |
extractROWS,Rle,RangeNSBS-method | Man page |
extractROWS,Rle,RleNSBS-method | Man page |
extractROWS,SortedByQueryHits,ANY-method | Man page |
extractROWS,TransposedDataFrame,ANY-method | Man page |
extractROWS,array,RangeNSBS-method | Man page |
extractROWS,data.frame,RangeNSBS-method | Man page |
extractROWS,vector_OR_factor,RangeNSBS-method | Man page |
extract_character_from_raw_by_positions | Source code |
extract_character_from_raw_by_ranges | Source code |
extract_data_frame_rows | Source code |
extract_positions_from_Rle | Source code |
extract_range_from_Rle | Source code |
extract_ranges_from_LLint | Source code |
extract_ranges_from_Rle | Source code |
extract_ranges_from_vector_OR_factor | Source code |
fancy_mseq | Source code |
filterRules | Man page |
filterRules,FilterMatrix-method | Man page |
findIntervalAndStartFromWidth | Source code |
findMatches | Man page |
findMatches,ANY,ANY-method | Man page |
findMatches,ANY,missing-method | Man page |
findRun | Man page |
findRun,Rle-method | Man page |
first | Man page |
first,Pairs-method | Man page |
first<- | Man page |
first<-,Pairs-method | Man page |
fold | Man page Source code |
formulaAsListCall | Source code |
formulaValues | Source code |
from | Man page |
from,Hits-method | Man page |
getDefaultSlotValue | Source code |
getListElement | Man page |
getListElement,List-method | Man page |
getListElement,TransposedDataFrame-method | Man page |
getListElement,list-method | Man page |
getStartEndRunAndOffset | Source code |
get_showHeadLines | Man page Source code |
get_showTailLines | Man page Source code |
groupsum | Source code |
gsub,ANY,ANY,Rle-method | Man page |
hasNonDefaultMethod | Source code |
hasS3Method | Source code |
head | Man page |
head,RectangularData-method | Man page |
head,Vector-method | Man page |
head.LLint | Source code |
head.RectangularData | Man page |
head.Vector | Man page Source code |
head_along_ROWS | Source code |
horizontal_slot_names | Man page |
horizontal_slot_names,DataFrame-method | Man page |
implodeIntBits | Source code |
intbitsAND | Source code |
intbitsNOT | Source code |
intbitsOR | Source code |
integer_OR_LLint | Man page |
integer_OR_LLint-class | Man page |
intersect,ANY,Rle-method | Man page |
intersect,Rle,ANY-method | Man page |
intersect,Rle,Rle-method | Man page |
intersect,Vector,Vector-method | Man page |
intersect.Vector | Man page Source code |
is.LLint | Man page Source code |
is.finite,Rle-method | Man page |
is.na,DataFrame-method | Man page |
is.na,LLint-method | Man page |
is.na,Rle-method | Man page |
is.na,Vector-method | Man page |
is.unsorted,Rle-method | Man page |
isConstant | Man page |
isConstant,array-method | Man page |
isConstant,integer-method | Man page |
isConstant,numeric-method | Man page |
isEmpty | Man page |
isEmpty,ANY-method | Man page |
isEmpty,List-method | Man page |
isNotSorted | Source code |
isNotStrictlySorted | Source code |
isNumericOrNAs | Source code |
isRecursive | Source code |
isRedundantHit | Man page Source code |
isSelfHit | Man page Source code |
isSequence | Man page Source code |
isSingleInteger | Man page Source code |
isSingleNumber | Man page Source code |
isSingleNumberOrNA | Man page Source code |
isSingleString | Man page Source code |
isSingleStringOrNA | Man page Source code |
isSorted | Man page |
isSorted,ANY-method | Man page |
isStrictlySorted | Man page |
isStrictlySorted,ANY-method | Man page |
isStrictlySorted,NSBS-method | Man page |
isStrictlySorted,RangeNSBS-method | Man page |
isStrictlySorted,Rle-method | Man page |
isStrictlySorted,RleNSBS-method | Man page |
isTRUEorFALSE | Man page Source code |
labeledLine | Source code |
lapply,List-method | Man page |
lapply,SimpleList-method | Man page |
last_or | Source code |
length,LLint-method | Man page |
length,NSBS-method | Man page |
length,RangeNSBS-method | Man page |
length,Rle-method | Man page |
length,RleNSBS-method | Man page |
length,TransposedDataFrame-method | Man page |
length,Vector-method | Man page |
lengths,Vector-method | Man page |
levels | Man page |
levels,Rle-method | Man page |
levels.Rle | Man page Source code |
levels<- | Man page |
levels<-,Factor-method | Man page |
levels<-,Rle-method | Man page |
listClassName | Source code |
list_OR_List | Man page |
list_OR_List-class | Man page |
lowestListElementClass | Source code |
lsubset_List_by_List | Source code |
mad,Rle-method | Man page |
mad.Rle | Man page |
makeAllGroupInnerHits | Source code |
makeAllGroupInnerHits.old | Source code |
makeClassinfoRowForCompactPrinting | Man page Source code |
makeEnvForNames | Source code |
makeFixedColumnEnv | Source code |
makeGlobalWarningEnv | Source code |
makeNakedCharacterMatrixForDisplay | Man page |
makeNakedCharacterMatrixForDisplay,ANY-method | Man page |
makeNakedCharacterMatrixForDisplay,DataFrame-method | Man page |
makeNakedCharacterMatrixForDisplay,Hits-method | Man page |
makeNakedCharacterMatrixForDisplay,Pairs-method | Man page |
makeNakedCharacterMatrixForDisplay,TransposedDataFrame-method | Man page |
makePowersOfTwo | Source code |
makePrettyMatrixForCompactPrinting | Man page Source code |
make_NA_LLint_ | Source code |
make_XYZxyz_to_XxYyZz_subscript | Source code |
make_class_info_for_DataFrame_display | Source code |
make_rownames_for_RectangularData_display | Source code |
make_zero_col_DFrame | Man page Source code |
map_inner_ROWS_to_list_elements | Source code |
map_positions_to_runs | Source code |
map_ranges_to_runs | Source code |
match | Man page |
match,ANY,Rle-method | Man page |
match,DataFrame,DataFrame-method | Man page |
match,Factor,Factor-method | Man page |
match,Factor,Vector-method | Man page |
match,Hits,Hits-method | Man page |
match,Pairs,Pairs-method | Man page |
match,Rle,ANY-method | Man page |
match,Rle,Rle-method | Man page |
match,Vector,Factor-method | Man page |
match,Vector,Vector-method | Man page |
matchIntegerPairs | Man page Source code |
matchIntegerQuads | Man page Source code |
mcols | Man page |
mcols,Vector-method | Man page |
mcols<- | Man page |
mcols<-,Vector-method | Man page |
mean,Rle-method | Man page |
mean.Rle | Man page Source code |
median,Rle-method | Man page |
median.Rle | Man page Source code |
mendoapply | Man page Source code |
merge | Man page |
merge,DataFrame,DataFrame-method | Man page |
merge,DataFrame,data.frame-method | Man page |
merge,Vector,Vector-method | Man page |
merge,data.frame,DataFrame-method | Man page |
mergeROWS | Man page |
mergeROWS,ANY,ANY-method | Man page |
mergeROWS,DataFrame,ANY-method | Man page |
mergeROWS,Vector,ANY-method | Man page |
metadata | Man page |
metadata,Annotated-method | Man page |
metadata<- | Man page |
metadata<-,Annotated-method | Man page |
missingArg | Source code |
mseq | Source code |
mstack | Man page |
mstack,DataFrame-method | Man page |
mstack,Vector-method | Man page |
mstack,vector-method | Man page |
nLnode | Man page |
nLnode,Hits-method | Man page |
nRnode | Man page |
nRnode,Hits-method | Man page |
na.exclude,DataFrame-method | Man page |
na.omit,DataFrame-method | Man page |
names,Factor-method | Man page |
names,Pairs-method | Man page |
names,SimpleList-method | Man page |
names,TransposedDataFrame-method | Man page |
names<-,Factor-method | Man page |
names<-,Pairs-method | Man page |
names<-,SimpleList-method | Man page |
names<-,TransposedDataFrame-method | Man page |
nchar,Rle-method | Man page |
ncol,DataFrame-method | Man page |
new2 | Man page Source code |
new_DataFrame | Source code |
new_Hits | Source code |
new_Rle | Source code |
new_SimpleList_from_list | Source code |
nlevels | Man page |
nlevels,Factor-method | Man page |
nnode | Man page |
nnode,SelfHits-method | Man page |
normSubsetIndex | Source code |
normalizeDoubleBracketSubscript | Man page Source code |
normalizeSingleBracketReplacementValue | Man page |
normalizeSingleBracketReplacementValue,ANY-method | Man page |
normalizeSingleBracketSubscript | Man page Source code |
normargRunK | Source code |
normargSingleEndOrNA | Source code |
normargSingleStartOrNA | Source code |
normargUseNames | Source code |
normarg_mcols | Source code |
normarg_method | Source code |
normarg_names | Source code |
nrow,DataFrame-method | Man page |
nrun | Man page |
nrun,Rle-method | Man page |
numeric2integer | Source code |
order,DataFrame-method | Man page |
order,Hits-method | Man page |
order,Pairs-method | Man page |
order,Rle-method | Man page |
orderBy | Source code |
orderIntegerPairs | Man page Source code |
orderIntegerQuads | Man page Source code |
parallelSlotNames | Man page Source code |
parallelVectorNames | Man page |
parallelVectorNames,ANY-method | Man page |
parallelVectorNames,List-method | Man page |
parallel_slot_names | Man page |
parallel_slot_names,Factor-method | Man page |
parallel_slot_names,FilterRules-method | Man page |
parallel_slot_names,Hits-method | Man page |
parallel_slot_names,Pairs-method | Man page |
parallel_slot_names,SimpleList-method | Man page |
parallel_slot_names,Vector-method | Man page |
params | Man page |
params,FilterClosure-method | Man page |
paste,Rle-method | Man page |
pc | Man page Source code |
pcompare | Man page |
pcompare,ANY,ANY-method | Man page |
pcompare,DataFrame,DataFrame-method | Man page |
pcompare,Factor,Factor-method | Man page |
pcompare,Factor,Vector-method | Man page |
pcompare,Hits,Hits-method | Man page |
pcompare,Pairs,Pairs-method | Man page |
pcompare,Vector,Factor-method | Man page |
pcompare,numeric,numeric-method | Man page |
pcompareIntegerPairs | Source code |
pmax,Rle-method | Man page |
pmax.int,Rle-method | Man page |
pmin,Rle-method | Man page |
pmin.int,Rle-method | Man page |
prepare_objects_to_bind | Source code |
printAtomicVectorInAGrid | Man page Source code |
quantile,Rle-method | Man page |
quantile.Rle | Man page Source code |
queryHits | Man page Source code |
queryHits,HitsList-method | Man page |
queryLength | Man page Source code |
quick_togroup | Source code |
quick_unlist | Source code |
quick_unsplit | Source code |
rank,Rle-method | Man page |
rank,Vector-method | Man page |
rbind,FilterMatrix-method | Man page |
rbind,List-method | Man page |
rbind,RectangularData-method | Man page |
rbind.RectangularData | Man page Source code |
rbind_mcols | Source code |
recycleArg | Man page Source code |
recycleCharacterArg | Man page Source code |
recycleIntegerArg | Man page Source code |
recycleLogicalArg | Man page Source code |
recycleNumericArg | Man page Source code |
recycleSingleBracketReplacementValue | Source code |
recycleVector | Source code |
relistToClass | Man page |
relistToClass,ANY-method | Man page |
relistToClass,DataFrame-method | Man page |
relistToClass,Hits-method | Man page |
relistToClass,SortedByQueryHits-method | Man page |
relistToClass,data.frame-method | Man page |
remapHits | Man page Source code |
rename | Man page |
rename,Vector-method | Man page |
rename,vector-method | Man page |
rep | Man page |
rep,Rle-method | Man page |
rep,Vector-method | Man page |
rep.int | Man page |
rep.int,Rle-method | Man page |
rep.int,Vector-method | Man page |
rep.int_along_ROWS | Source code |
repROWS | Source code |
replaceCOLS | Man page |
replaceROWS | Man page |
replaceROWS,ANY,ANY-method | Man page |
replaceROWS,DataFrame,ANY-method | Man page |
replaceROWS,Rle,ANY-method | Man page |
replaceROWS,Vector,ANY-method | Man page |
rev | Man page |
rev,Rle-method | Man page |
rev,Vector-method | Man page |
rev.Rle | Man page Source code |
rev.Vector | Man page |
revElements | Man page |
revElements,List-method | Man page |
revElements,list-method | Man page |
revROWS | Source code |
reverseIntegerInjection | Source code |
reverseSelfmatchMapping | Source code |
revmap_Hits | Source code |
rownames,DataFrame-method | Man page |
rownames<-,DataFrame-method | Man page |
runEndsOfIntegerPairs | Source code |
runLength | Man page |
runLength,Rle-method | Man page |
runLength<- | Man page |
runLength<-,Rle-method | Man page |
runValue | Man page |
runValue,Rle-method | Man page |
runValue<- | Man page |
runValue<-,Rle-method | Man page |
runmean | Man page |
runmean,Rle-method | Man page |
runmed,Rle-method | Man page |
runq | Man page |
runq,Rle-method | Man page |
runsum | Man page |
runsum,Rle-method | Man page |
runwtsum | Man page |
runwtsum,Rle-method | Man page |
safeEval | Source code |
safeExplode | Man page Source code |
sameAsPreviousROW | Man page |
sameAsPreviousROW,ANY-method | Man page |
sameAsPreviousROW,DataFrame-method | Man page |
sameAsPreviousROW,Pairs-method | Man page |
sapply,List-method | Man page |
sapply_NROW | Source code |
sapply_isNULL | Source code |
sd,Rle-method | Man page |
second | Man page |
second,Pairs-method | Man page |
second<- | Man page |
second<-,Pairs-method | Man page |
selectHits | Man page Source code |
selectSome | Source code |
selfmatch | Man page |
selfmatch,ANY-method | Man page |
selfmatch,Factor-method | Man page |
selfmatch,Vector-method | Man page |
selfmatch,factor-method | Man page |
selfmatchIntegerPairs | Man page Source code |
selfmatchIntegerQuads | Man page Source code |
setDefaultSlotValue | Source code |
setListElement | Man page |
setListElement,List-method | Man page |
setListElement,list-method | Man page |
setListElement_default | Source code |
setMethods | Man page Source code |
setPrototypeFromObject | Source code |
setReplaceAs | Source code |
setValidity2 | Man page Source code |
set_unlisted_names | Source code |
setdiff,ANY,Rle-method | Man page |
setdiff,Rle,ANY-method | Man page |
setdiff,Rle,Rle-method | Man page |
setdiff,Vector,Vector-method | Man page |
setdiff.Vector | Man page Source code |
setequal,Vector,Vector-method | Man page |
setequal.Vector | Man page Source code |
shiftApply | Man page |
shiftApply,Vector,Vector-method | Man page |
shiftApply,vector,vector-method | Man page |
shiftApply-methods | Man page |
show,DataFrame-method | Man page |
show,Factor-method | Man page |
show,FilterClosure-method | Man page |
show,FilterMatrix-method | Man page |
show,Hits-method | Man page |
show,LLint-method | Man page |
show,List-method | Man page |
show,Pairs-method | Man page |
show,RangeNSBS-method | Man page |
show,Rle-method | Man page |
show,TransposedDataFrame-method | Man page |
show-utils | Man page |
showAsCell | Man page |
showAsCell,ANY-method | Man page |
showAsCell,AsIs-method | Man page |
showAsCell,DataFrame-method | Man page |
showAsCell,Factor-method | Man page |
showAsCell,LLint-method | Man page |
showAsCell,List-method | Man page |
showAsCell,character-method | Man page |
showAsCell,data.frame-method | Man page |
showAsCell,list-method | Man page |
showAsCell,numeric-method | Man page |
showAsCell_array | Source code |
showAsCell_list | Source code |
showPairs | Source code |
sketchStr | Source code |
smoothEnds,Rle-method | Man page |
sort,DataFrame-method | Man page |
sort,Rle-method | Man page |
sort,SortedByQueryHits-method | Man page |
sort,Vector-method | Man page |
sort.DataFrame | Man page |
sort.List | Source code |
sort.Rle | Man page Source code |
sort.Vector | Man page Source code |
sortedIntegerPairs | Source code |
sortedIntegerQuads | Source code |
sortedMerge | Source code |
space | Man page |
space,HitsList-method | Man page |
split | Man page |
split,ANY,Vector-method | Man page |
split,Vector,ANY-method | Man page |
split,Vector,Vector-method | Man page |
split,list,Vector-method | Man page |
splitAsList | Man page |
splitAsList,ANY,ANY-method | Man page |
splitAsList,SortedByQueryHits,ANY-method | Man page |
stack,List-method | Man page |
stack,matrix-method | Man page |
stack-methods | Man page |
stack_index | Source code |
start,Rle-method | Man page |
sub,ANY,ANY,Rle-method | Man page |
subjectHits | Man page Source code |
subjectHits,HitsList-method | Man page |
subjectLength | Man page Source code |
subset | Man page |
subset,RectangularData-method | Man page |
subset,Vector-method | Man page |
subset.Vector | Man page Source code |
subsetByFilter | Man page |
subsetByFilter,ANY,FilterRules-method | Man page |
subset_List_by_List | Source code |
subset_Vector | Source code |
subset_along_ROWS | Source code |
subsetting-utils | Man page |
substr,Rle-method | Man page |
substring,Rle-method | Man page |
summary,FilterMatrix-method | Man page |
summary,FilterRules-method | Man page |
summary,Hits-method | Man page |
summary,Rle-method | Man page |
summary,Vector-method | Man page |
summary.Hits | Man page Source code |
summary.Rle | Man page Source code |
summary.Vector | Man page Source code |
svn.time | Man page Source code |
t,DataFrame-method | Man page |
t,Hits-method | Man page |
t,HitsList-method | Man page |
t,TransposedDataFrame-method | Man page |
t.DataFrame | Man page Source code |
t.Hits | Man page Source code |
t.HitsList | Source code |
t.TransposedDataFrame | Man page Source code |
table,Rle-method | Man page |
table,Vector-method | Man page |
tabulate,Rle-method | Man page |
tabulate2 | Source code |
tail | Man page |
tail,RectangularData-method | Man page |
tail,Vector-method | Man page |
tail.LLint | Source code |
tail.RectangularData | Man page |
tail.Vector | Man page Source code |
tail_along_ROWS | Source code |
to | Man page |
to,Hits-method | Man page |
toListOfIntegerVectors | Man page Source code |
toNumSnippet | Source code |
tolower,Rle-method | Man page |
top_prenv | Source code |
top_prenv_dots | Source code |
toupper,Rle-method | Man page |
transform,DataFrame-method | Man page |
transform,Vector-method | Man page |
transform.DataFrame | Man page |
transform.Vector | Man page |
transformColumns | Source code |
unfactor | Man page |
unfactor,Factor-method | Man page |
unfactor,factor-method | Man page |
union,ANY,Rle-method | Man page |
union,Rle,ANY-method | Man page |
union,Rle,Rle-method | Man page |
union,SortedByQueryHits,Hits-method | Man page |
union,Vector,Vector-method | Man page |
union.Vector | Man page Source code |
unique,DataFrame-method | Man page |
unique,Rle-method | Man page |
unique,Vector-method | Man page |
unique.DataFrame | Man page |
unique.Vector | Man page Source code |
unlist,List-method | Man page |
unstrsplit | Man page |
unstrsplit,character-method | Man page |
unstrsplit,list-method | Man page |
updateObject,DataFrame-method | Man page |
updateObject,Hits-method | Man page |
updateObject,Vector-method | Man page |
values | Man page |
values,Vector-method | Man page |
values<- | Man page |
values<-,Vector-method | Man page |
var,Rle,Rle-method | Man page |
var,Rle,missing-method | Man page |
vector_OR_Vector | Man page |
vector_OR_Vector-class | Man page |
vector_OR_factor | Man page |
vector_OR_factor-class | Man page |
vertical_slot_names | Man page |
vertical_slot_names,DataFrame-method | Man page |
which,Rle-method | Man page |
which.max,Rle-method | Man page |
width,Rle-method | Man page |
window | Man page |
window,Vector-method | Man page |
window.LLint | Source code |
window.Vector | Man page Source code |
window_along_ROWS | Source code |
within,List-method | Man page |
wmsg | Man page Source code |
wmsg2 | Source code |
xtabs,DataFrame-method | Man page |
xtfrm,Factor-method | Man page |
xtfrm,Rle-method | Man page |
xtfrm,Vector-method | Man page |
zipdown | Man page |
zipdown,ANY-method | Man page |
zipdown,List-method | Man page |
zipup | Man page |
zipup,ANY,ANY-method | Man page |
zipup,Pairs,missing-method | Man page |
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