# S4 implementation of vectors and lists

## Documentation for package ‘S4Vectors’ version 0.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I L M N O P Q R S T U V W X Z misc

## -- A --

active | Collection of Filter Rules
active-method | Collection of Filter Rules
active<- | Collection of Filter Rules
active<--method | Collection of Filter Rules
aggregate | Compute summary statistics of subsets of vector-like objects
aggregate-method | Compute summary statistics of subsets of vector-like objects
aggregate-methods | Compute summary statistics of subsets of vector-like objects
aggregate.Vector | Compute summary statistics of subsets of vector-like objects
Annotated | Annotated class
Annotated-class | Annotated class
anyDuplicated-method | Subsetting utilities
anyDuplicated.NSBS | Subsetting utilities
append-method | Collection of Filter Rules
append-method | Rle objects
append-method | Vector objects
as.character-method | Vector objects
as.complex-method | Vector objects
as.data.frame-method | DataFrame objects
as.data.frame-method | List objects
as.data.frame-method | Pairs objects
as.data.frame-method | Rle objects
as.data.frame-method | Vector objects
as.data.frame.Vector | Vector objects
as.double-method | Vector objects
as.env | DataTable objects
as.env-method | DataTable objects
as.env-method | Vector objects
as.factor-method | Rle objects
as.integer-method | Vector objects
as.integer-method | Subsetting utilities
as.list-method | List objects
as.list-method | Rle objects
as.list-method | SimpleList objects
as.list-method | Vector objects
as.list.Vector | Vector objects
as.logical-method | Vector objects
as.matrix-method | DataFrame objects
as.matrix-method | Hits objects
as.matrix-method | List of Hits objects
as.numeric-method | Vector objects
as.raw-method | Vector objects
as.table-method | Hits objects
as.table-method | List of Hits objects
as.vector-method | Rle objects
as.vectorORfactor | Rle objects
as.vectorORfactor-method | Rle objects

## -- B --

breakTies | Hits objects
by-method | DataTable objects

## -- C --

c-method | Collection of Filter Rules
c-method | Hits objects
c-method | Pairs objects
c-method | Rle objects
c-method | SimpleList objects
cbind-method | DataFrame objects
cbind-method | DataTable objects
cbind-method | Matrix for Filter Results
cbind-method | Common operations on List objects
chartr-method | Common operations on Rle objects
class:DataFrame | DataFrame objects
class:DataTable | DataTable objects
class:DataTableORNULL | Vector objects
class:expressionORfunction | Collection of Filter Rules
class:FilterRules | Collection of Filter Rules
class:Hits | Hits objects
class:HitsList | List of Hits objects
class:List | List objects
class:NSBS | Subsetting utilities
class:Pairs | Pairs objects
class:Rle | Rle objects
class:SelfHits | Hits objects
class:SelfHitsList | List of Hits objects
class:SimpleList | SimpleList objects
class:SortedByQueryHits | Hits objects
class:SortedByQueryHitsList | List of Hits objects
class:SortedByQuerySelfHits | Hits objects
class:SortedByQuerySelfHitsList | List of Hits objects
class:Vector | Vector objects
classNameForDisplay | Vector objects
classNameForDisplay-method | Hits objects
classNameForDisplay-method | SimpleList objects
classNameForDisplay-method | Vector objects
coerce-method | DataFrame objects
coerce-method | Collection of Filter Rules
coerce-method | Hits objects
coerce-method | List objects
coerce-method | Pairs objects
coerce-method | Rle objects
coerce-method | SimpleList objects
coerce-method | Vector objects
colnames-method | DataFrame objects
colnames<--method | DataFrame objects
compare | Compare, order, tabulate vector-like objects
complete.cases-method | DataTable objects
Complex-method | Common operations on Rle objects
cor-method | Common operations on Rle objects
countLnodeHits | Hits objects
countLnodeHits-method | Hits objects
countMatches | Compare, order, tabulate vector-like objects
countMatches-method | Compare, order, tabulate vector-like objects
countQueryHits | Hits objects
countRnodeHits | Hits objects
countRnodeHits-method | Hits objects
countSubjectHits | Hits objects
cov-method | Common operations on Rle objects

## -- D --

DataFrame | DataFrame objects
DataFrame-class | DataFrame objects
DataTable | DataTable objects
DataTable-class | DataTable objects
DataTableORNULL | Vector objects
DataTableORNULL-class | Vector objects
decode | Rle objects
decode-method | Rle objects
diff-method | Common operations on Rle objects
diff.Rle | Common operations on Rle objects
dim-method | DataTable objects
dimnames-method | DataTable objects
dimnames<--method | DataTable objects
duplicated-method | DataTable objects
duplicated-method | Rle objects
duplicated-method | Compare, order, tabulate vector-like objects
duplicated.DataTable | DataTable objects
duplicated.Vector | Compare, order, tabulate vector-like objects

## -- E --

elementLengths | List objects
elementLengths-method | List objects
elementMetadata | Vector objects
elementMetadata-method | Vector objects
elementMetadata<- | Vector objects
elementMetadata<--method | Vector objects
elementNROWS | List objects
elementNROWS-method | List objects
elementType | List objects
elementType-method | List objects
end-method | Rle objects
endoapply | Common operations on List objects
endoapply-method | Common operations on List objects
endoapply-method | SimpleList objects
eval-method | Collection of Filter Rules
evalSeparately | Collection of Filter Rules
evalSeparately-method | Collection of Filter Rules
expand | Unlist the list-like columns of a DataFrame object
expand-method | Unlist the list-like columns of a DataFrame object
expressionORfunction | Collection of Filter Rules
expressionORfunction-class | Collection of Filter Rules
extractROWS | Subsetting utilities
extractROWS-method | Hits objects
extractROWS-method | Rle objects
extractROWS-method | Subsetting utilities

## -- F --

Filter-method | Common operations on List objects
FilterMatrix | Matrix for Filter Results
FilterMatrix-class | Matrix for Filter Results
FilterRules | Collection of Filter Rules
filterRules | Matrix for Filter Results
FilterRules-class | Collection of Filter Rules
filterRules-method | Matrix for Filter Results
Find-method | Common operations on List objects
findMatches | Compare, order, tabulate vector-like objects
findMatches-method | Compare, order, tabulate vector-like objects
findRun | Rle objects
findRun-method | Rle objects
first | Pairs objects
first-method | Pairs objects
first<- | Pairs objects
first<--method | Pairs objects
from | Hits objects
from-method | Hits objects

## -- G --

getListElement | Subsetting utilities
gsub-method | Common operations on Rle objects

## -- H --

head | Vector objects
head-method | Vector objects
head.DataTable | DataTable objects
head.Vector | Vector objects
Hits | Hits objects
Hits-class | Hits objects
Hits-comparison | Comparing and ordering hits
Hits-setops | Set operations on Hits objects
HitsList | List of Hits objects
HitsList-class | List of Hits objects

## -- I --

ifelse-method | Common operations on Rle objects
intersect-method | Rle objects
intersect-method | Set operations on vector-like objects
IQR-method | Common operations on Rle objects
is.na-method | DataTable objects
is.na-method | Rle objects
is.unsorted-method | Rle objects
isConstant | Test if a vector-like object is sorted
isConstant-method | Test if a vector-like object is sorted
isEmpty | List objects
isEmpty-method | List objects
isRedundantHit | Hits objects
isSelfHit | Hits objects
isSorted | Test if a vector-like object is sorted
isSorted-method | Test if a vector-like object is sorted
isStrictlySorted | Test if a vector-like object is sorted
isStrictlySorted-method | Test if a vector-like object is sorted
isStrictlySorted-method | Subsetting utilities

## -- L --

lapply-method | Common operations on List objects
lapply-method | SimpleList objects
length-method | Pairs objects
length-method | Rle objects
length-method | SimpleList objects
length-method | Vector objects
length-method | Subsetting utilities
lengths-method | Vector objects
levels-method | Common operations on Rle objects
levels.Rle | Common operations on Rle objects
levels<--method | Common operations on Rle objects
List | List objects
List-class | List objects
List-utils | Common operations on List objects

## -- M --

mad-method | Common operations on Rle objects
mad.Rle | Common operations on Rle objects
Map-method | Common operations on List objects
match-method | Comparing and ordering hits
match-method | Pairs objects
match-method | Rle objects
Math-method | Common operations on Rle objects
Math2-method | Common operations on Rle objects
mcols | Vector objects
mcols-method | Vector objects
mcols<- | Vector objects
mcols<--method | Vector objects
mean-method | Common operations on Rle objects
mean.Rle | Common operations on Rle objects
median-method | Common operations on Rle objects
median.Rle | Common operations on Rle objects
mendoapply | Common operations on List objects
mendoapply-method | Common operations on List objects
mendoapply-method | SimpleList objects
merge | Merge vector-like objects
merge-method | DataTable objects
merge-method | Merge vector-like objects
metadata | Annotated class
metadata-method | Annotated class
metadata<- | Annotated class
metadata<--method | Annotated class

## -- N --

na.exclude-method | DataTable objects
na.omit-method | DataTable objects
names-method | Pairs objects
names-method | SimpleList objects
names<--method | Pairs objects
names<--method | SimpleList objects
nchar-method | Common operations on Rle objects
NCOL-method | DataTable objects
ncol-method | DataFrame objects
nLnode | Hits objects
nLnode-method | Hits objects
nnode | Hits objects
nnode-method | Hits objects
normalizeDoubleBracketSubscript | Subsetting utilities
normalizeSingleBracketReplacementValue | Subsetting utilities
normalizeSingleBracketReplacementValue-method | Subsetting utilities
normalizeSingleBracketSubscript | Subsetting utilities
nRnode | Hits objects
nRnode-method | Hits objects
NROW-method | DataTable objects
NROW-method | Vector objects
nrow-method | DataFrame objects
nrun | Rle objects
nrun-method | Rle objects
NSBS | Subsetting utilities
NSBS-class | Subsetting utilities
NSBS-method | Subsetting utilities

## -- O --

Ops-method | Common operations on Rle objects
order-method | Comparing and ordering hits
order-method | Rle objects

## -- P --

Pairs | Pairs objects
Pairs-class | Pairs objects
parallelSlotNames-method | Hits objects
parallelSlotNames-method | Pairs objects
parallelVectorNames | Vector objects
parallelVectorNames-method | List objects
parallelVectorNames-method | Vector objects
params | Collection of Filter Rules
params-method | Collection of Filter Rules
paste-method | Common operations on Rle objects
pc | Common operations on List objects
pcompare | Compare, order, tabulate vector-like objects
pcompare-method | Comparing and ordering hits
pmax-method | Common operations on Rle objects
pmax.int-method | Common operations on Rle objects
pmin-method | Common operations on Rle objects
pmin.int-method | Common operations on Rle objects
Position-method | Common operations on List objects

## -- Q --

quantile-method | Common operations on Rle objects
quantile.Rle | Common operations on Rle objects
queryHits | Hits objects
queryHits-method | List of Hits objects
queryLength | Hits objects

## -- R --

rank-method | Compare, order, tabulate vector-like objects
rbind-method | DataFrame objects
rbind-method | DataTable objects
rbind-method | Matrix for Filter Results
rbind-method | Common operations on List objects
Reduce-method | Common operations on List objects
relistToClass | List objects
relistToClass-method | List of Hits objects
relistToClass-method | List objects
remapHits | Hits objects
rename | Vector objects
rename-method | Vector objects
rep-method | Rle objects
rep.int-method | Rle objects
replaceROWS | Subsetting utilities
replaceROWS-method | Vector objects
replaceROWS-method | Subsetting utilities
rev-method | Rle objects
rev.Rle | Rle objects
revElements | Common operations on List objects
revElements-method | Common operations on List objects
Rle | Rle objects
Rle-class | Rle objects
Rle-method | Rle objects
Rle-runstat | Fixed-width running window summaries
Rle-utils | Common operations on Rle objects
ROWNAMES | DataTable objects
ROWNAMES-method | DataTable objects
ROWNAMES-method | Vector objects
rownames-method | DataFrame objects
rownames<--method | DataFrame objects
runLength | Rle objects
runLength-method | Rle objects
runLength<- | Rle objects
runLength<--method | Rle objects
runmean | Fixed-width running window summaries
runmean-method | Fixed-width running window summaries
runmed-method | Fixed-width running window summaries
runq | Fixed-width running window summaries
runq-method | Fixed-width running window summaries
runsum | Fixed-width running window summaries
runsum-method | Fixed-width running window summaries
runValue | Rle objects
runValue-method | Rle objects
runValue<- | Rle objects
runValue<--method | Rle objects
runwtsum | Fixed-width running window summaries
runwtsum-method | Fixed-width running window summaries

## -- S --

safeExplode | Some utility functions to operate on strings
sapply-method | Common operations on List objects
sd-method | Common operations on Rle objects
second | Pairs objects
second-method | Pairs objects
second<- | Pairs objects
second<--method | Pairs objects
SelfHits | Hits objects
SelfHits-class | Hits objects
SelfHitsList | List of Hits objects
SelfHitsList-class | List of Hits objects
selfmatch | Compare, order, tabulate vector-like objects
selfmatch-method | Compare, order, tabulate vector-like objects
setdiff-method | Rle objects
setdiff-method | Set operations on vector-like objects
setequal-method | Set operations on vector-like objects
setListElement | Subsetting utilities
shiftApply | Apply a function over subsequences of 2 vector-like objects
shiftApply-method | Apply a function over subsequences of 2 vector-like objects
shiftApply-methods | Apply a function over subsequences of 2 vector-like objects
show-method | DataTable objects
show-method | Matrix for Filter Results
show-method | Collection of Filter Rules
show-method | Hits objects
show-method | List objects
show-method | Pairs objects
show-method | Rle objects
show-method | Subsetting utilities
showAsCell | Vector objects
showAsCell-method | Rle objects
showAsCell-method | Vector objects
SimpleList | SimpleList objects
SimpleList-class | SimpleList objects
smoothEnds-method | Fixed-width running window summaries
sort-method | Rle objects
sort-method | Compare, order, tabulate vector-like objects
sort.Vector | Compare, order, tabulate vector-like objects
SortedByQueryHits | Hits objects
SortedByQueryHits-class | Hits objects
SortedByQueryHitsList | List of Hits objects
SortedByQueryHitsList-class | List of Hits objects
SortedByQuerySelfHits | Hits objects
SortedByQuerySelfHits-class | Hits objects
SortedByQuerySelfHitsList | List of Hits objects
SortedByQuerySelfHitsList-class | List of Hits objects
space | List of Hits objects
space-method | List of Hits objects
split | Divide a vector-like object into groups
split-method | Divide a vector-like object into groups
split-methods | Divide a vector-like object into groups
start-method | Rle objects
strsplitAsListOfIntegerVectors | Some utility functions to operate on strings
sub-method | Common operations on Rle objects
subjectHits | Hits objects
subjectHits-method | List of Hits objects
subjectLength | Hits objects
subset-method | DataTable objects
subsetByFilter | Collection of Filter Rules
subsetByFilter-method | Collection of Filter Rules
subsetting-utils | Subsetting utilities
substr-method | Common operations on Rle objects
substring-method | Common operations on Rle objects
Summary-method | Common operations on Rle objects
summary-method | Matrix for Filter Results
summary-method | Collection of Filter Rules
summary-method | Common operations on Rle objects
summary.Rle | Common operations on Rle objects
svn.time | Some utility functions to operate on strings

## -- T --

t-method | Hits objects
t-method | List of Hits objects
table-method | Rle objects
table-method | Compare, order, tabulate vector-like objects
tabulate-method | Rle objects
tail | Vector objects
tail-method | Vector objects
tail.DataTable | DataTable objects
tail.Vector | Vector objects
to | Hits objects
to-method | Hits objects
tolower-method | Common operations on Rle objects
toupper-method | Common operations on Rle objects

## -- U --

union-method | Set operations on Hits objects
union-method | Rle objects
union-method | Set operations on vector-like objects
unique-method | DataTable objects
unique-method | Rle objects
unique-method | Compare, order, tabulate vector-like objects
unique.DataTable | DataTable objects
unique.Vector | Compare, order, tabulate vector-like objects
unlist-method | List objects
unstrsplit | Some utility functions to operate on strings
unstrsplit-method | Some utility functions to operate on strings
updateObject-method | Hits objects

## -- V --

values | Vector objects
values-method | Vector objects
values<- | Vector objects
values<--method | Vector objects
var-method | Common operations on Rle objects
Vector | Vector objects
Vector-class | Vector objects
Vector-comparison | Compare, order, tabulate vector-like objects
Vector-merge | Merge vector-like objects
Vector-setops | Set operations on vector-like objects

## -- W --

which-method | Common operations on Rle objects
which.max-method | Common operations on Rle objects
width-method | Rle objects
window | Vector objects
window-method | Vector objects
window.Vector | Vector objects
within-method | Common operations on List objects

## -- X --

xtabs-method | DataTable objects

## -- Z --

zipdown | Convert between parallel vectors and lists
zipdown-method | Convert between parallel vectors and lists
zipup | Convert between parallel vectors and lists
zipup-method | Pairs objects
zipup-method | Convert between parallel vectors and lists

## -- misc --

!-method | Common operations on Rle objects
!=-method | Compare, order, tabulate vector-like objects
$-method | List objects
$<--method | List objects
%in%-method | Rle objects
%in%-method | Compare, order, tabulate vector-like objects
<-method | Compare, order, tabulate vector-like objects
<=-method | Compare, order, tabulate vector-like objects
==-method | Compare, order, tabulate vector-like objects
>-method | Compare, order, tabulate vector-like objects
>=-method | Compare, order, tabulate vector-like objects
[-method | DataFrame objects
[-method | Matrix for Filter Results
[-method | Collection of Filter Rules
[-method | List objects
[-method | Rle objects
[-method | Vector objects
[<--method | DataFrame objects
[<--method | List objects
[<--method | Rle objects
[<--method | Vector objects
[[-method | List objects
[[<--method | DataFrame objects
[[<--method | Collection of Filter Rules
[[<--method | List objects