Representation and manipulation of genomic intervals and variables defined along a genome

Documentation for package ‘GenomicRanges’ version 1.30.1

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

-- A --

absoluteRanges	Transform genomic ranges into "absolute" ranges
as.character-method	GRanges objects
as.data.frame-method	Memory-efficient representation of genomic positions
as.data.frame-method	GRanges objects
as.factor-method	GRanges objects

-- B --

bindAsGRanges	Manipulating genomic variables
binnedAverage	Manipulating genomic variables

-- C --

c-method	GRanges objects
checkConstraint	Enforcing constraints thru Constraint objects
class:Constraint	Enforcing constraints thru Constraint objects
class:Constraint_OR_NULL	Enforcing constraints thru Constraint objects
class:DelegatingGenomicRanges	DelegatingGenomicRanges objects
class:GenomicRanges	GRanges objects
class:GenomicRangesList	GenomicRangesList objects
class:GNCList	GNCList objects
class:GPos	Memory-efficient representation of genomic positions
class:GRanges	GRanges objects
class:GRangesList	GRangesList objects
class:IRanges_OR_IPos	GRanges objects
class:SimpleGenomicRangesList	GenomicRangesList objects
coerce-method	GNCList objects
coerce-method	Memory-efficient representation of genomic positions
coerce-method	GRanges objects
coerce-method	GRangesList objects
coerce-method	Manipulating genomic variables
coerce-method	Make a GRanges object from a data.frame or DataFrame
Constraint	Enforcing constraints thru Constraint objects
constraint	Enforcing constraints thru Constraint objects
Constraint-class	Enforcing constraints thru Constraint objects
constraint<-	Enforcing constraints thru Constraint objects
Constraints	Enforcing constraints thru Constraint objects
Constraint_OR_NULL	Enforcing constraints thru Constraint objects
Constraint_OR_NULL-class	Enforcing constraints thru Constraint objects
countOverlaps	Finding overlapping genomic ranges
countOverlaps-method	Finding overlapping genomic ranges
coverage	Coverage of a GRanges or GRangesList object
coverage-method	Coverage of a GRanges or GRangesList object
coverage-methods	Coverage of a GRanges or GRangesList object

-- D --

DelegatingGenomicRanges-class	DelegatingGenomicRanges objects
disjoin	Inter range transformations of a GRanges or GRangesList object
disjoin-method	Inter range transformations of a GRanges or GRangesList object
disjointBins	Inter range transformations of a GRanges or GRangesList object
disjointBins-method	Inter range transformations of a GRanges or GRangesList object
distance	Finding the nearest genomic range neighbor
distance-method	Finding the nearest genomic range neighbor
distanceToNearest	Finding the nearest genomic range neighbor
distanceToNearest-method	Finding the nearest genomic range neighbor
duplicated-method	Comparing and ordering genomic ranges
duplicated.GenomicRanges	Comparing and ordering genomic ranges

-- E --

elementMetadata-method	GRangesList objects
elementMetadata<--method	GRangesList objects
end-method	GNCList objects
end-method	GRanges objects
end-method	GRangesList objects
end<--method	GRanges objects
end<--method	GRangesList objects

-- F --

findOverlaps	Finding overlapping genomic ranges
findOverlaps-method	Finding overlapping genomic ranges
findOverlaps-methods	Finding overlapping genomic ranges
flank	Intra range transformations of a GRanges or GRangesList object
flank-method	Intra range transformations of a GRanges or GRangesList object
follow	Finding the nearest genomic range neighbor
follow-method	Finding the nearest genomic range neighbor

-- G --

gaps	Inter range transformations of a GRanges or GRangesList object
gaps-method	Inter range transformations of a GRanges or GRangesList object
genomic-range-squeezers	Squeeze the genomic ranges out of a range-based object
GenomicRanges	GRanges objects
GenomicRanges-class	GRanges objects
GenomicRanges-comparison	Comparing and ordering genomic ranges
GenomicRangesList	GenomicRangesList objects
GenomicRangesList-class	GenomicRangesList objects
GenomicRanges_OR_GRangesList-class	GRangesList objects
GenomicRanges_OR_missing-class	GRanges objects
genomicvariables	Manipulating genomic variables
genomicvars	Manipulating genomic variables
GNCList	GNCList objects
GNCList-class	GNCList objects
GPos	Memory-efficient representation of genomic positions
GPos-class	Memory-efficient representation of genomic positions
GRanges	GRanges objects
granges	Squeeze the genomic ranges out of a range-based object
GRanges-class	GRanges objects
granges-method	GNCList objects
granges-method	GRanges objects
GRangesList	GRangesList objects
GRangesList-class	GRangesList objects
grglist	Squeeze the genomic ranges out of a range-based object
grglist-method	Squeeze the genomic ranges out of a range-based object

-- I --

inter-range-methods	Inter range transformations of a GRanges or GRangesList object
intersect	Set operations on genomic ranges
intersect-method	Set operations on genomic ranges
intra-range-methods	Intra range transformations of a GRanges or GRangesList object
invertStrand-method	Strand utilities
IRanges_OR_IPos	GRanges objects
IRanges_OR_IPos-class	GRanges objects
is.unsorted-method	Comparing and ordering genomic ranges
isDisjoint	Inter range transformations of a GRanges or GRangesList object
isDisjoint-method	Inter range transformations of a GRanges or GRangesList object
isSmallGenome	Transform genomic ranges into "absolute" ranges

-- L --

length-method	GNCList objects
length-method	GRanges objects

-- M --

makeGRangesFromDataFrame	Make a GRanges object from a data.frame or DataFrame
makeGRangesListFromDataFrame	Make a GRangesList object from a data.frame or DataFrame
makeGRangesListFromFeatureFragments	GRangesList objects
match-method	Comparing and ordering genomic ranges
mcolAsRleList	Manipulating genomic variables

-- N --

names-method	GNCList objects
names-method	Memory-efficient representation of genomic positions
names-method	GRanges objects
names<--method	Memory-efficient representation of genomic positions
names<--method	GRanges objects
narrow	Intra range transformations of a GRanges or GRangesList object
narrow-method	Intra range transformations of a GRanges or GRangesList object
nearest	Finding the nearest genomic range neighbor
nearest-method	Finding the nearest genomic range neighbor
nearest-methods	Finding the nearest genomic range neighbor

-- O --

Ops-method	Intra range transformations of a GRanges or GRangesList object
order-method	Comparing and ordering genomic ranges
overlapsAny	Finding overlapping genomic ranges

-- P --

pcompare	Comparing and ordering genomic ranges
pcompare-method	Comparing and ordering genomic ranges
pgap	Set operations on genomic ranges
pgap-method	Set operations on genomic ranges
phicoef	Calculate the "phi coefficient" between two binary variables
pintersect	Set operations on genomic ranges
pintersect-method	Set operations on genomic ranges
pos-method	Memory-efficient representation of genomic positions
precede	Finding the nearest genomic range neighbor
precede-method	Finding the nearest genomic range neighbor
promoters	Intra range transformations of a GRanges or GRangesList object
promoters-method	Intra range transformations of a GRanges or GRangesList object
psetdiff	Set operations on genomic ranges
psetdiff-method	Set operations on genomic ranges
punion	Set operations on genomic ranges
punion-method	Set operations on genomic ranges

-- R --

range	Inter range transformations of a GRanges or GRangesList object
range-method	Inter range transformations of a GRanges or GRangesList object
ranges-method	DelegatingGenomicRanges objects
ranges-method	GNCList objects
ranges-method	GRanges objects
ranges-method	GRangesList objects
ranges<--method	GRanges objects
ranges<--method	GRangesList objects
rank-method	Comparing and ordering genomic ranges
reduce	Inter range transformations of a GRanges or GRangesList object
reduce-method	Inter range transformations of a GRanges or GRangesList object
relativeRanges	Transform genomic ranges into "absolute" ranges
relistToClass-method	GRangesList objects
resize	Intra range transformations of a GRanges or GRangesList object
resize-method	Intra range transformations of a GRanges or GRangesList object
restrict	Intra range transformations of a GRanges or GRangesList object
restrict-method	Intra range transformations of a GRanges or GRangesList object

-- S --

score-method	GRanges objects
score-method	GRangesList objects
score<--method	GRanges objects
score<--method	GRangesList objects
selfmatch-method	Comparing and ordering genomic ranges
seqinfo-method	DelegatingGenomicRanges objects
seqinfo-method	GNCList objects
seqinfo-method	GRanges objects
seqinfo-method	GRangesList objects
seqinfo<--method	GRanges objects
seqinfo<--method	GRangesList objects
seqnames-method	DelegatingGenomicRanges objects
seqnames-method	GNCList objects
seqnames-method	GRanges objects
seqnames-method	GRangesList objects
seqnames<--method	GRanges objects
seqnames<--method	GRangesList objects
setdiff	Set operations on genomic ranges
setdiff-method	Set operations on genomic ranges
setops-methods	Set operations on genomic ranges
shift	Intra range transformations of a GRanges or GRangesList object
shift-method	Intra range transformations of a GRanges or GRangesList object
show-method	Memory-efficient representation of genomic positions
show-method	GRanges objects
show-method	GRangesList objects
SimpleGenomicRangesList-class	GenomicRangesList objects
slidingWindows	Generate windows for a GenomicRanges
slidingWindows-method	Generate windows for a GenomicRanges
sort-method	Comparing and ordering genomic ranges
sort.GenomicRanges	Comparing and ordering genomic ranges
start-method	GNCList objects
start-method	GRanges objects
start-method	GRangesList objects
start<--method	GRanges objects
start<--method	GRangesList objects
strand-method	DelegatingGenomicRanges objects
strand-method	GNCList objects
strand-method	GRanges objects
strand-method	GRangesList objects
strand-method	Strand utilities
strand-utils	Strand utilities
strand<--method	GRanges objects
strand<--method	GRangesList objects
strand<--method	Strand utilities
subsetByOverlaps	Finding overlapping genomic ranges
summary-method	GRanges objects
summary.GenomicRanges	GRanges objects

-- T --

tile	Generate windows for a GenomicRanges
tile-method	Generate windows for a GenomicRanges
tile-methods	Generate windows for a GenomicRanges
tileGenome	Put (virtual) tiles on a given genome
trim-method	Intra range transformations of a GRanges or GRangesList object

-- U --

union	Set operations on genomic ranges
union-method	Set operations on genomic ranges
updateObject-method	Memory-efficient representation of genomic positions
updateObject-method	GRanges objects
updateObject-method	GRangesList objects

-- W --

width-method	GNCList objects
width-method	GRanges objects
width-method	GRangesList objects
width<--method	GRanges objects
width<--method	GRangesList objects
window-method	GRanges objects

-- misc --

$-method	GRanges objects
$<--method	GRanges objects
[-method	GRanges objects
[-method	GRangesList objects
[<--method	GRanges objects
[<--method	GRangesList objects
[[<--method	GRangesList objects