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

## Documentation for package ‘GenomicRanges’ version 1.28.6

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

## Help Pages

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 | GPos objects
as.data.frame-method | GRanges objects
as.factor-method | GRanges objects

## -- B --

bindAsGRanges | Manipulating genomic variables
binnedAverage | Manipulating genomic variables

## -- C --

c-method | GPos objects
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 | GPos objects
class:GRanges | GRanges objects
class:GRangesList | GRangesList objects
class:SimpleGenomicRangesList | GenomicRangesList objects
coerce-method | GNCList objects
coerce-method | GPos objects
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 | GPos objects
end-method | GRanges objects
end-method | GRangesList objects
end<--method | GRanges objects
end<--method | GRangesList objects
extractROWS-method | GPos 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
GenomicRanges | GRanges objects
GenomicRanges-class | GRanges objects
GenomicRanges-comparison | Comparing and ordering genomic ranges
GenomicRangesList | GenomicRangesList objects
GenomicRangesList-class | GenomicRangesList objects
GenomicRangesORGRangesList-class | GRanges objects
GenomicRangesORmissing-class | GRanges objects
genomicvariables | Manipulating genomic variables
genomicvars | Manipulating genomic variables
GNCList | GNCList objects
GNCList-class | GNCList objects
GPos | GPos objects
GPos-class | GPos objects
GRanges | GRanges objects
granges | Squeeze the 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 ranges out of a range-based object
grglist-method | Squeeze the 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
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 | GPos 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 | GPos objects
names-method | GRanges objects
names<--method | GPos objects
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 | GPos objects
pos-method | GPos objects
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
range-squeezers | Squeeze the ranges out of a range-based object
ranges-method | DelegatingGenomicRanges objects
ranges-method | GNCList objects
ranges-method | GPos 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
rglist | Squeeze the ranges out of a range-based object
rglist-method | Squeeze the ranges out of a range-based 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 | GPos objects
seqinfo-method | GRanges objects
seqinfo-method | GRangesList objects
seqinfo<--method | GPos objects
seqinfo<--method | GRanges objects
seqinfo<--method | GRangesList objects
seqnames-method | DelegatingGenomicRanges objects
seqnames-method | GNCList objects
seqnames-method | GPos 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 | GPos objects
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 | GPos 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 | GPos 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 | GRanges objects
updateObject-method | GRangesList objects

## -- W --

width-method | GNCList objects
width-method | GPos 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