S4 implementation of vector-like and list-like objects

[Up] [Top]

Documentation for package ‘S4Vectors’ version 0.16.0

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
anyNA-method Vector objects
append-method Collection of Filter Rules
append-method Rle objects
append-method Vector objects
as.character-method LLint vectors
as.character-method Vector objects
as.character.LLint LLint vectors
as.complex-method Vector objects
as.data.frame-method DataFrame objects
as.data.frame-method DataTable 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.DataTable DataTable 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 LLint vectors
as.integer-method Vector objects
as.integer-method Subsetting utilities
as.integer.LLint LLint vectors
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.LLint LLint vectors
as.logical-method LLint vectors
as.logical-method Vector objects
as.logical.LLint LLint vectors
as.matrix-method DataFrame objects
as.matrix-method Hits objects
as.matrix-method List of Hits objects
as.matrix-method Vector objects
as.matrix.Vector Vector objects
as.numeric-method LLint vectors
as.numeric-method Vector objects
as.numeric.LLint LLint vectors
as.raw-method Vector objects
as.table-method Hits objects
as.table-method List of Hits objects
as.vector-method Rle objects
as.vector.Rle Rle objects

-- B --

breakTies Hits objects
by-method DataTable objects

-- C --

c-method Collection of Filter Rules
c-method Hits objects
c-method LLint vectors
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:DataTable_OR_NULL Vector objects
class:expression_OR_function 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:LLint LLint vectors
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 Display utilities
classNameForDisplay-method Hits objects
classNameForDisplay-method SimpleList objects
classNameForDisplay-method Display utilities
coerce-method DataFrame objects
coerce-method Collection of Filter Rules
coerce-method Hits objects
coerce-method LLint vectors
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
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
DataTable_OR_NULL Vector objects
DataTable_OR_NULL-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
droplevels-method Common operations on List objects
droplevels-method Common operations on Rle objects
droplevels.List Common operations on List objects
droplevels.Rle Common operations on Rle 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 --

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
expand.grid Vector objects
expand.grid-method Vector objects
expression_OR_function Collection of Filter Rules
expression_OR_function-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 --

intersect-method Rle objects
intersect-method Set operations on vector-like objects
intersect.Vector Set operations on vector-like objects
IQR-method Common operations on Rle objects
is.LLint LLint vectors
is.na-method DataTable objects
is.na-method LLint vectors
is.na-method Rle objects
is.na-method Vector 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 LLint vectors
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
LLint LLint vectors
LLint-class LLint vectors

-- 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
NA_LLint_ LLint vectors
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 LLint vectors
Ops-method Common operations on Rle objects
order-method Comparing and ordering hits

-- 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
setdiff.Vector Set operations on vector-like objects
setequal-method Set operations on vector-like objects
setequal.Vector 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 LLint vectors
show-method List objects
show-method Pairs objects
show-method Rle objects
show-method Subsetting utilities
show-utils Display utilities
showAsCell Display utilities
showAsCell-method LLint vectors
showAsCell-method Rle objects
showAsCell-method Display utilities
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 LLint vectors
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
transform-method DataTable objects
transform.DataTable DataTable objects

-- U --

union-method Set operations on Hits objects
union-method Rle objects
union-method Set operations on vector-like objects
union.Vector 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 DataFrame objects
[[-method List objects
[[<--method DataFrame objects
[[<--method Collection of Filter Rules
[[<--method List objects