Representation and Manipulation of Genomic Tuples


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Documentation for package ‘GenomicTuples’ version 1.24.0

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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
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