Representation and Manipulation of Genomic Tuples

---

Documentation for package ‘GenomicTuples’ version 1.43.1

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

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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
GenomicTuples	Representation and manipulation of genomic tuples.
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