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

## Documentation for package ‘GenomicRanges’ version 1.22.0

- 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 V W misc

## -- A --

absoluteRanges | Transform genomic ranges into "absolute" ranges
as.character-method | GRanges objects
as.data.frame-method | GRanges objects
as.factor-method | GRanges objects
assay | SummarizedExperiment instances
assay-method | SummarizedExperiment instances
assay<- | SummarizedExperiment instances
assay<--method | SummarizedExperiment instances
assayNames | SummarizedExperiment instances
assayNames-method | SummarizedExperiment instances
assayNames<- | SummarizedExperiment instances
assayNames<--method | SummarizedExperiment instances
assays | SummarizedExperiment instances
Assays-class | SummarizedExperiment instances
assays-method | SummarizedExperiment instances
assays<- | SummarizedExperiment instances
assays<--method | SummarizedExperiment instances

## -- B --

bindAsGRanges | Manipulating genomic variables
binnedAverage | Manipulating genomic variables

## -- C --

c-method | GRanges objects
cbind-method | SummarizedExperiment instances
checkConstraint | Enforcing constraints thru Constraint objects
class:Constraint | Enforcing constraints thru Constraint objects
class:ConstraintORNULL | Enforcing constraints thru Constraint objects
class:DelegatingGenomicRanges | DelegatingGenomicRanges objects
class:GenomicRanges | GRanges objects
class:GenomicRangesList | GenomicRangesList objects
class:GIntervalTree | GIntervalTree objects
class:GNCList | GNCList objects
class:GRanges | GRanges objects
class:GRangesList | GRangesList objects
class:SimpleGenomicRangesList | GenomicRangesList objects
coerce-method | GIntervalTree objects
coerce-method | GNCList objects
coerce-method | GRanges objects
coerce-method | GRangesList objects
coerce-method | GenomicRangesList objects
coerce-method | SummarizedExperiment instances
coerce-method | Manipulating genomic variables
coerce-method | Make a GRanges object from a data.frame or DataFrame
colData | SummarizedExperiment instances
colData-method | SummarizedExperiment instances
colData<- | SummarizedExperiment instances
colData<--method | SummarizedExperiment instances
compare | Comparing and ordering genomic ranges
compare-method | Comparing and ordering genomic ranges
compare-method | SummarizedExperiment instances
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
ConstraintORNULL | Enforcing constraints thru Constraint objects
ConstraintORNULL-class | Enforcing constraints thru Constraint objects
Constraints | Enforcing constraints thru Constraint objects
countOverlaps | Finding overlapping genomic ranges
countOverlaps-method | SummarizedExperiment instances
countOverlaps-method | Finding overlapping genomic ranges
coverage | Coverage of a GRanges or GRangesList object
coverage-method | SummarizedExperiment instances
coverage-method | Coverage of a GRanges or GRangesList object
coverage-methods | Coverage of a GRanges or GRangesList object

## -- D --

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

## -- E --

elementMetadata-method | GIntervalTree objects
elementMetadata-method | GRangesList objects
elementMetadata-method | SummarizedExperiment instances
elementMetadata<--method | GRanges objects
elementMetadata<--method | GRangesList objects
elementMetadata<--method | SummarizedExperiment instances
end-method | GIntervalTree objects
end-method | GNCList objects
end-method | GRanges objects
end-method | GRangesList objects
end-method | SummarizedExperiment instances
end<--method | GRanges objects
end<--method | GRangesList objects
end<--method | SummarizedExperiment instances
exptData | SummarizedExperiment instances
exptData-method | SummarizedExperiment instances
exptData<- | SummarizedExperiment instances
exptData<--method | SummarizedExperiment instances

## -- F --

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

## -- G --

gaps | Inter range transformations of a GenomicRanges or GRangesList object
gaps-method | Inter range transformations of a GenomicRanges 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
GIntervalTree | GIntervalTree objects
GIntervalTree-class | GIntervalTree objects
GNCList | GNCList objects
GNCList-class | GNCList 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
granges-method | SummarizedExperiment instances
GRangesList | GRangesList objects
GRangesList-class | GRangesList objects
grglist | Squeeze the ranges out of a range-based object

## -- I --

inter-range-methods | Inter range transformations of a GenomicRanges or GRangesList object
intersect-method | Set operations on GRanges and GRangesList objects
intra-range-methods | Intra range transformations of a GRanges or GRangesList object
isDisjoint | Inter range transformations of a GenomicRanges or GRangesList object
isDisjoint-method | SummarizedExperiment instances
isDisjoint-method | Inter range transformations of a GenomicRanges 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
makeGRangesListFromFeatureFragments | GRangesList objects
makeSummarizedExperimentFromExpressionSet | Make a SummarizedExperiment object from an ExpressionSet
mapCoords | Mapping ranges between sequences
mapCoords-method | Mapping ranges between sequences
mapCoords-methods | Mapping ranges between sequences
match-method | Comparing and ordering genomic ranges
mcolAsRleList | Manipulating genomic variables
mcols-method | SummarizedExperiment instances
mcols<--method | SummarizedExperiment instances

## -- N --

names-method | GIntervalTree objects
names-method | GNCList objects
names-method | GRanges objects
names<--method | GRanges objects
narrow | Intra range transformations of a GRanges or GRangesList object
narrow-method | SummarizedExperiment instances
narrow-method | Intra range transformations of a GRanges or GRangesList object
nearest | Finding the nearest genomic range neighbor
nearest-method | SummarizedExperiment instances
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
order-method | SummarizedExperiment instances
overlapsAny | Finding overlapping genomic ranges
overlapsAny-method | SummarizedExperiment instances
overlapsAny-method | Finding overlapping genomic ranges

## -- P --

pgap | Set operations on GRanges and GRangesList objects
pgap-method | Set operations on GRanges and GRangesList objects
phicoef | Calculate the "phi coefficient" between two binary variables
pintersect | Set operations on GRanges and GRangesList objects
pintersect-method | Set operations on GRanges and GRangesList objects
pmapCoords | Mapping ranges between sequences
pmapCoords-method | Mapping ranges between sequences
precede | Finding the nearest genomic range neighbor
precede-method | SummarizedExperiment instances
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 GRanges and GRangesList objects
psetdiff-method | Set operations on GRanges and GRangesList objects
punion | Set operations on GRanges and GRangesList objects
punion-method | Set operations on GRanges and GRangesList objects

## -- R --

range | Inter range transformations of a GenomicRanges or GRangesList object
range-method | Inter range transformations of a GenomicRanges or GRangesList object
range-squeezers | Squeeze the ranges out of a range-based object
ranges-method | DelegatingGenomicRanges objects
ranges-method | GIntervalTree objects
ranges-method | GNCList objects
ranges-method | GRanges objects
ranges-method | GRangesList objects
ranges-method | SummarizedExperiment instances
ranges<--method | GRanges objects
ranges<--method | GRangesList objects
ranges<--method | SummarizedExperiment instances
rank-method | Comparing and ordering genomic ranges
rank-method | SummarizedExperiment instances
rbind-method | SummarizedExperiment instances
reduce | Inter range transformations of a GenomicRanges or GRangesList object
reduce-method | Inter range transformations of a GenomicRanges 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 | SummarizedExperiment instances
resize-method | Intra range transformations of a GRanges or GRangesList object
restrict | Intra range transformations of a GRanges or GRangesList object
restrict-method | SummarizedExperiment instances
restrict-method | Intra range transformations of a GRanges or GRangesList object
rglist | Squeeze the ranges out of a range-based object
rowData | SummarizedExperiment instances
rowData<- | SummarizedExperiment instances
rowRanges | SummarizedExperiment instances
rowRanges-method | SummarizedExperiment instances
rowRanges<- | SummarizedExperiment instances
rowRanges<--method | SummarizedExperiment instances

## -- S --

score-method | GIntervalTree objects
score-method | GRanges objects
score-method | GRangesList objects
score<--method | GRanges objects
score<--method | GRangesList objects
seqinfo-method | DelegatingGenomicRanges objects
seqinfo-method | GIntervalTree objects
seqinfo-method | GNCList objects
seqinfo-method | GRanges objects
seqinfo-method | GRangesList objects
seqinfo-method | SummarizedExperiment instances
seqinfo<--method | GRanges objects
seqinfo<--method | GRangesList objects
seqinfo<--method | SummarizedExperiment instances
seqnames-method | DelegatingGenomicRanges objects
seqnames-method | GIntervalTree objects
seqnames-method | GNCList objects
seqnames-method | GRanges objects
seqnames-method | GRangesList objects
seqnames-method | SummarizedExperiment instances
seqnames<--method | GRanges objects
seqnames<--method | GRangesList objects
setdiff-method | Set operations on GRanges and GRangesList objects
setops-methods | Set operations on GRanges and GRangesList objects
ShallowData-class | SummarizedExperiment instances
ShallowSimpleListAssays-class | SummarizedExperiment instances
shift | Intra range transformations of a GRanges or GRangesList object
shift-method | SummarizedExperiment instances
shift-method | Intra range transformations of a GRanges or GRangesList object
show-method | GIntervalTree objects
show-method | GRanges objects
show-method | GRangesList objects
show-method | SummarizedExperiment instances
SimpleGenomicRangesList-class | GenomicRangesList objects
sort-method | Comparing and ordering genomic ranges
sort-method | SummarizedExperiment instances
sort.GenomicRanges | Comparing and ordering genomic ranges
split-method | SummarizedExperiment instances
start-method | GIntervalTree objects
start-method | GNCList objects
start-method | GRanges objects
start-method | GRangesList objects
start-method | SummarizedExperiment instances
start<--method | GRanges objects
start<--method | GRangesList objects
start<--method | SummarizedExperiment instances
strand-method | DelegatingGenomicRanges objects
strand-method | GIntervalTree objects
strand-method | GNCList objects
strand-method | GRanges objects
strand-method | GRangesList objects
strand-method | SummarizedExperiment instances
strand-method | Strand utilities
strand-utils | Strand utilities
strand<--method | GRanges objects
strand<--method | GRangesList objects
strand<--method | SummarizedExperiment instances
strand<--method | Strand utilities
subset-method | SummarizedExperiment instances
subsetByOverlaps | Finding overlapping genomic ranges
subsetByOverlaps-method | SummarizedExperiment instances
subsetByOverlaps-method | Finding overlapping genomic ranges
SummarizedExperiment | SummarizedExperiment instances
SummarizedExperiment-class | SummarizedExperiment instances
SummarizedExperiment-method | SummarizedExperiment instances

## -- T --

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

## -- U --

union-method | Set operations on GRanges and GRangesList objects
update-method | DelegatingGenomicRanges objects
updateObject-method | GRanges objects
updateObject-method | GRangesList objects
updateObject-method | SummarizedExperiment instances

## -- V --

values-method | SummarizedExperiment instances
values<--method | SummarizedExperiment instances

## -- W --

width-method | GIntervalTree objects
width-method | GNCList objects
width-method | GRanges objects
width-method | GRangesList objects
width-method | SummarizedExperiment instances
width<--method | GRanges objects
width<--method | GRangesList objects
width<--method | SummarizedExperiment instances
window-method | GRanges objects

## -- misc --

$-method | GRanges objects
$-method | SummarizedExperiment instances
$<--method | GRanges objects
$<--method | SummarizedExperiment instances
[-method | GIntervalTree objects
[-method | GRanges objects
[-method | GRangesList objects
[-method | SummarizedExperiment instances
[<--method | GRanges objects
[<--method | GRangesList objects
[<--method | SummarizedExperiment instances
[[-method | SummarizedExperiment instances
[[<--method | GRangesList objects
[[<--method | SummarizedExperiment instances