# Representation and Manipulation of Genomic Tuples

## Documentation for package ‘GenomicTuples’ version 1.20.0

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

## Help Pages

A C D E F G I L M N O P R S T U W misc

GenomicTuples-package | Representation and manipulation of genomic tuples.

## -- A --

as.character-method | GTuples objects
as.data.frame-method | GTuples objects
as.factor-method | GTuples objects

## -- C --

c-method | GTuples objects
class:GTuples | GTuples objects
class:GTuplesList | GTuplesList objects
coerce-method | GTuples objects
coerce-method | GTuplesList objects
countOverlaps | Finding overlapping genomic tuples
countOverlaps-method | Finding overlapping genomic tuples
coverage-method | Undefined methods

## -- D --

disjoin-method | Undefined methods
disjointBins-method | Undefined methods
distance-method | Finding the nearest genomic tuple/range neighbour
distanceToNearest-method | Finding the nearest genomic tuple/range neighbour
duplicated-method | Comparing and ordering genomic tuples
duplicated.GTuples | Comparing and ordering genomic tuples

## -- E --

elementMetadata-method | GTuplesList objects
elementMetadata<--method | GTuples objects
elementMetadata<--method | GTuplesList objects
end-method | GTuples objects
end-method | GTuplesList objects
end<--method | GTuples objects
end<--method | GTuplesList objects

## -- F --

findOverlaps | Finding overlapping genomic tuples
findOverlaps-method | Finding overlapping genomic tuples
findOverlaps-methods | Finding overlapping genomic tuples
flank-method | Undefined methods
follow-method | Finding the nearest genomic tuple/range neighbour

## -- G --

gaps-method | Undefined methods
granges-method | GTuples objects
gtlist | Squeeze the tuples out of a tuples-based object
GTuples | GTuples objects
gtuples | Squeeze the tuples out of a tuples-based object
GTuples-class | GTuples objects
GTuples-comparison | Comparing and ordering genomic tuples
GTuplesList | GTuplesList objects
GTuplesList-class | GTuplesList objects

## -- I --

intersect-method | Undefined methods
intra-tuple-methods | Intra-tuple transformations of a GTuples or GTuplesLists object
IPD | GTuples objects
IPD-method | GTuples objects
IPD-method | GTuplesList objects
is.unsorted-method | Comparing and ordering genomic tuples
isDisjoint-method | Undefined methods

## -- L --

length-method | GTuples objects

## -- M --

match-method | Comparing and ordering genomic tuples

## -- N --

names-method | GTuples objects
names<--method | GTuples objects
narrow | Undefined methods
narrow-method | Undefined methods
nearest-method | Finding the nearest genomic tuple/range neighbour
nearest-methods | Finding the nearest genomic tuple/range neighbour

## -- O --

Ops-method | Undefined methods
order-method | Comparing and ordering genomic tuples
overlapsAny | Finding overlapping genomic tuples
overlapsAny-method | Finding overlapping genomic tuples

## -- P --

pcompare-method | Comparing and ordering genomic tuples
pgap-method | Undefined methods
pintersect-method | Undefined methods
precede-method | Finding the nearest genomic tuple/range neighbour
promoters-method | Undefined methods
psetdiff-method | Undefined methods
punion-method | Undefined methods

## -- R --

range-method | Undefined methods
ranges-method | GTuples objects
ranges-method | GTuplesList objects
ranges<--method | GTuples objects
ranges<--method | GTuplesList objects
rank-method | Comparing and ordering genomic tuples
reduce-method | Undefined methods
relistToClass-method | GTuplesList objects
replaceROWS-method | Undefined methods
resize-method | Undefined methods
restrict-method | Undefined methods

## -- S --

score-method | GTuples objects
score-method | GTuplesList objects
score<--method | GTuples objects
score<--method | GTuplesList objects
selfmatch-method | Comparing and ordering genomic tuples
seqinfo-method | GTuples objects
seqinfo-method | GTuplesList objects
seqinfo<--method | GTuples objects
seqinfo<--method | GTuplesList objects
seqnames-method | GTuples objects
seqnames-method | GTuplesList objects
seqnames<--method | GTuples objects
seqnames<--method | GTuplesList objects
setdiff-method | Undefined methods
shift | Intra-tuple transformations of a GTuples or GTuplesLists object
shift-method | Intra-tuple transformations of a GTuples or GTuplesLists object
show-method | GTuples objects
size | GTuples objects
size-method | GTuples objects
size-method | GTuplesList objects
sort-method | Comparing and ordering genomic tuples
sort.GTuples | Comparing and ordering genomic tuples
start-method | GTuples objects
start-method | GTuplesList objects
start<--method | GTuples objects
start<--method | GTuplesList objects
strand-method | GTuples objects
strand-method | GTuplesList objects
strand<--method | GTuples objects
strand<--method | GTuplesList objects
subsetByOverlaps | Finding overlapping genomic tuples
subsetByOverlaps-method | Finding overlapping genomic tuples

## -- T --

tile-method | Undefined methods
trim-method | Intra-tuple transformations of a GTuples or GTuplesLists object
tuples | GTuples objects
tuples-method | GTuples objects
tuples-method | GTuplesList objects
tuples-squeezers | Squeeze the tuples out of a tuples-based object
tuples<- | GTuples objects
tuples<--method | GTuples objects
tuples<--method | GTuplesList objects

## -- U --

union-method | Undefined methods
updateObject-method | GTuples objects
updateObject-method | GTuplesList objects

## -- W --

width-method | GTuples objects
width-method | GTuplesList objects
width<--method | GTuples objects
width<--method | GTuplesList objects
window-method | GTuples objects

## -- misc --

$-method | GTuples objects
$<--method | GTuples objects
[-method | GTuples objects
[-method | GTuplesList objects
[<--method | GTuples objects
[<--method | GTuplesList objects
[[<--method | GTuplesList objects