# Representation and manipulation of genomic intervals

## Documentation for package ‘GenomicRanges’ version 1.14.3

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

## Help Pages

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

## -- A --

as.data.frame-method | GAlignments objects
as.data.frame-method | GAlignmentsList objects
as.data.frame-method | GRanges objects
as.data.frame-method | GRangesList objects
as.data.frame-method | Seqinfo objects
assay | SummarizedExperiment instances
assay-method | SummarizedExperiment instances
assay<- | SummarizedExperiment instances
assay<--method | SummarizedExperiment instances
assays | SummarizedExperiment instances
Assays-class | SummarizedExperiment instances
assays-method | SummarizedExperiment instances
assays<- | SummarizedExperiment instances
assays<--method | SummarizedExperiment instances

## -- C --

c-method | GAlignmentPairs objects
c-method | GAlignments objects
c-method | GAlignmentsList objects
c-method | GRanges objects
cbind-method | SummarizedExperiment instances
checkConstraint | Enforcing constraints thru Constraint objects
cigar | GAlignments objects
cigar-method | GAlignments objects
cigar-method | GAlignmentsList objects
cigar-utils | CIGAR utility functions
cigarNarrow | CIGAR utility functions
cigarOpTable | CIGAR utility functions
cigarQNarrow | CIGAR utility functions
cigarRangesAlongPairwiseSpace | CIGAR utility functions
cigarRangesAlongQuerySpace | CIGAR utility functions
cigarRangesAlongReferenceSpace | CIGAR utility functions
cigarToCigarTable | CIGAR utility functions
cigarToIRanges | CIGAR utility functions
cigarToIRangesListByAlignment | CIGAR utility functions
cigarToIRangesListByRName | CIGAR utility functions
cigarToQWidth | CIGAR utility functions
cigarToRleList | CIGAR utility functions
cigarToWidth | CIGAR utility functions
cigarWidthAlongPairwiseSpace | CIGAR utility functions
cigarWidthAlongQuerySpace | CIGAR utility functions
cigarWidthAlongReferenceSpace | CIGAR utility functions
CIGAR_OPS | CIGAR utility functions
class:Constraint | Enforcing constraints thru Constraint objects
class:ConstraintORNULL | Enforcing constraints thru Constraint objects
class:GAlignmentPairs | GAlignmentPairs objects
class:GAlignments | GAlignments objects
class:GAlignmentsList | GAlignmentsList objects
class:GappedAlignmentPairs | GAlignmentPairs objects
class:GappedAlignments | GAlignments objects
class:GenomicRanges | GRanges objects
class:GenomicRangesList | GenomicRangesList objects
class:GIntervalTree | GIntervalTree objects
class:GRanges | GRanges objects
class:GRangesList | GRangesList objects
class:Seqinfo | Seqinfo objects
class:SimpleGenomicRangesList | GenomicRangesList objects
coerce-method | GAlignmentPairs objects
coerce-method | GAlignments objects
coerce-method | GAlignmentsList objects
coerce-method | GIntervalTree objects
coerce-method | GRanges objects
coerce-method | GRangesList objects
coerce-method | GenomicRangesList objects
coerce-method | Seqinfo objects
coerce-method | Make a GRanges object from a data.frame or DataFrame
coerce-method | Mapping ranges between sequences
colData | SummarizedExperiment instances
colData-method | SummarizedExperiment instances
colData<- | SummarizedExperiment instances
colData<--method | SummarizedExperiment instances
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
countCompatibleOverlaps | encodeOverlaps method for GRangesList objects, and related utilities
countMatches-method | Comparing and ordering genomic ranges
countMatches-method | Finding overlapping genomic ranges
countOverlaps-method | SummarizedExperiment instances
countOverlaps-method | Finding overlapping genomic ranges
coverage-method | SummarizedExperiment instances
coverage-method | Coverage of a GRanges, GRangesList, GAlignments, or GAlignmentPairs object
coverage-methods | Coverage of a GRanges, GRangesList, GAlignments, or GAlignmentPairs object

## -- D --

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

## -- E --

elementMetadata-method | GAlignmentsList objects
elementMetadata-method | GIntervalTree objects
elementMetadata-method | GRangesList objects
elementMetadata-method | SummarizedExperiment instances
elementMetadata<--method | GAlignmentPairs objects
elementMetadata<--method | GAlignments objects
elementMetadata<--method | GAlignmentsList objects
elementMetadata<--method | GRanges objects
elementMetadata<--method | GRangesList objects
elementMetadata<--method | SummarizedExperiment instances
encodeOverlaps-method | encodeOverlaps method for GRangesList objects, and related utilities
encodeOverlaps-methods | encodeOverlaps method for GRangesList objects, and related utilities
end-method | GAlignments objects
end-method | GAlignmentsList objects
end-method | GIntervalTree 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
explodeCigarOpLengths | CIGAR utility functions
explodeCigarOps | CIGAR utility functions
exptData | SummarizedExperiment instances
exptData-method | SummarizedExperiment instances
exptData<- | SummarizedExperiment instances
exptData<--method | SummarizedExperiment instances
extractAlignmentRangesOnReference | CIGAR utility functions
extractQueryStartInTranscript | encodeOverlaps method for GRangesList objects, and related utilities
extractSkippedExonRanks | encodeOverlaps method for GRangesList objects, and related utilities
extractSkippedExonRanks-method | encodeOverlaps method for GRangesList objects, and related utilities
extractSpannedExonRanks | encodeOverlaps method for GRangesList objects, and related utilities
extractSpannedExonRanks-method | encodeOverlaps method for GRangesList objects, and related utilities
extractSteppedExonRanks | encodeOverlaps method for GRangesList objects, and related utilities
extractSteppedExonRanks-method | encodeOverlaps method for GRangesList objects, and related utilities

## -- F --

findCompatibleOverlaps | encodeOverlaps method for GRangesList objects, and related utilities
findCompatibleOverlaps-method | encodeOverlaps method for GRangesList objects, and related utilities
findMatches-method | Comparing and ordering genomic ranges
findMatches-method | Finding overlapping genomic ranges
findOverlaps-method | SummarizedExperiment instances
findOverlaps-method | Finding overlapping genomic ranges
findOverlaps-methods | Finding overlapping genomic ranges
findSpliceOverlaps | Classify ranges (reads) as compatible with existing genomic annotations or as having novel splice events
findSpliceOverlaps-method | Classify ranges (reads) as compatible with existing genomic annotations or as having novel splice events
findSpliceOverlaps-methods | Classify ranges (reads) as compatible with existing genomic annotations or as having novel splice events
first | GAlignmentPairs objects
first-method | GAlignmentPairs objects
flank-method | GRangesList objects
flank-method | SummarizedExperiment instances
flank-method | Intra range transformations of a GenomicRanges object
flipQuery | encodeOverlaps method for GRangesList objects, and related utilities
follow-method | SummarizedExperiment instances
follow-method | Finding the nearest genomic range neighbor

## -- G --

GAlignmentPairs | GAlignmentPairs objects
GAlignmentPairs-class | GAlignmentPairs objects
GAlignments | GAlignments objects
GAlignments-class | GAlignments objects
GAlignmentsList | GAlignmentsList objects
GAlignmentsList-class | GAlignmentsList objects
GappedAlignmentPairs | GAlignmentPairs objects
GappedAlignmentPairs-class | GAlignmentPairs objects
GappedAlignments | GAlignments objects
GappedAlignments-class | GAlignments objects
gaps-method | Inter range transformations of a GenomicRanges object
genome | Accessing/modifying sequence information
genome-method | Seqinfo objects
genome-method | Accessing/modifying sequence information
genome<- | Accessing/modifying sequence information
genome<--method | Seqinfo objects
genome<--method | Accessing/modifying sequence information
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
GIntervalTree | GIntervalTree objects
GIntervalTree-class | GIntervalTree objects
GRanges | GRanges objects
granges | GAlignments objects
GRanges-class | GRanges objects
granges-method | GAlignmentPairs objects
granges-method | GAlignments objects
granges-method | GAlignmentsList objects
granges-method | SummarizedExperiment instances
granges-method | Mapping ranges between sequences
GRangesList | GRangesList objects
GRangesList-class | GRangesList objects
grglist | GAlignments objects
grglist-method | GAlignmentPairs objects
grglist-method | GAlignments objects
grglist-method | GAlignmentsList objects

## -- I --

inter-range-methods | Inter range transformations of a GenomicRanges object
intersect-method | Seqinfo objects
intersect-method | Set operations on GRanges/GRangesList/GAlignments objects
IntersectionNotEmpty | Perform overlap queries between reads and genomic features
IntersectionStrict | Perform overlap queries between reads and genomic features
intra-range-methods | Intra range transformations of a GenomicRanges object
introns | GAlignments objects
introns-method | GAlignmentPairs objects
introns-method | GAlignments objects
introns-method | GAlignmentsList objects
isCircular | Accessing/modifying sequence information
isCircular-method | Seqinfo objects
isCircular-method | Accessing/modifying sequence information
isCircular<- | Accessing/modifying sequence information
isCircular<--method | Seqinfo objects
isCircular<--method | Accessing/modifying sequence information
isCompatibleWithSkippedExons | encodeOverlaps method for GRangesList objects, and related utilities
isCompatibleWithSkippedExons-method | encodeOverlaps method for GRangesList objects, and related utilities
isCompatibleWithSplicing | encodeOverlaps method for GRangesList objects, and related utilities
isCompatibleWithSplicing-method | encodeOverlaps method for GRangesList objects, and related utilities
isDisjoint-method | GRangesList objects
isDisjoint-method | SummarizedExperiment instances
isDisjoint-method | Inter range transformations of a GenomicRanges object
isProperPair | GAlignmentPairs objects
isProperPair-method | GAlignmentPairs objects

## -- K --

keepSeqlevels | seqlevels utility functions

## -- L --

last | GAlignmentPairs objects
last-method | GAlignmentPairs objects
left | GAlignmentPairs objects
left-method | GAlignmentPairs objects
length-method | GAlignmentPairs objects
length-method | GAlignments objects
length-method | GRanges objects
length-method | Seqinfo objects

## -- M --

makeGAlignmentsListFromFeatureFragments | GAlignmentsList objects
makeGRangesFromDataFrame | Make a GRanges object from a data.frame or DataFrame
makeGRangesListFromFeatureFragments | GRangesList objects
makeSeqnameIds | Assign sequence IDs to sequence names
map-method | Mapping ranges between sequences
match-method | Comparing and ordering genomic ranges
match-method | SummarizedExperiment instances
match-method | Finding overlapping genomic ranges
mcols-method | SummarizedExperiment instances
mcols<--method | SummarizedExperiment instances
merge-method | Seqinfo objects

## -- N --

names-method | GAlignmentPairs objects
names-method | GAlignments objects
names-method | GAlignmentsList objects
names-method | GIntervalTree objects
names-method | GRanges objects
names-method | Seqinfo objects
names<--method | GAlignmentPairs objects
names<--method | GAlignments objects
names<--method | GAlignmentsList objects
names<--method | GRanges objects
names<--method | Seqinfo objects
narrow-method | SummarizedExperiment instances
narrow-method | Intra range transformations of a GenomicRanges object
nearest-method | SummarizedExperiment instances
nearest-method | Finding the nearest genomic range neighbor
nearest-methods | Finding the nearest genomic range neighbor
ngap-method | GAlignmentPairs objects
ngap-method | GAlignments objects
ngap-method | GAlignmentsList objects

## -- O --

Ops-method | Intra range transformations of a GenomicRanges object
order-method | Comparing and ordering genomic ranges
order-method | SummarizedExperiment instances
overlapsAny-method | SummarizedExperiment instances
overlapsAny-method | Finding overlapping genomic ranges

## -- P --

pgap-method | Set operations on GRanges/GRangesList/GAlignments objects
phicoef | Calculate the "phi coefficient" between two binary variables
pintersect-method | Set operations on GRanges/GRangesList/GAlignments objects
precede-method | SummarizedExperiment instances
precede-method | Finding the nearest genomic range neighbor
promoters-method | GRangesList objects
promoters-method | Intra range transformations of a GenomicRanges object
psetdiff-method | Set operations on GRanges/GRangesList/GAlignments objects
punion-method | Set operations on GRanges/GRangesList/GAlignments objects

## -- Q --

qnarrow | GAlignments objects
qnarrow-method | GAlignments objects
qnarrow-method | GAlignmentsList objects
queryLoc2refLoc | CIGAR utility functions
queryLocs2refLocs | CIGAR utility functions
qwidth | GAlignments objects
qwidth-method | GAlignments objects
qwidth-method | GAlignmentsList objects

## -- R --

range-method | GRangesList objects
range-method | Inter range transformations of a GenomicRanges object
ranges-method | GAlignments objects
ranges-method | GAlignmentsList objects
ranges-method | GIntervalTree 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
readGAlignmentPairs | GAlignmentPairs objects
readGAlignments | GAlignments objects
readGAlignmentsList | GAlignmentsList objects
readGappedAlignmentPairs | GAlignmentPairs objects
readGappedAlignments | GAlignments objects
reduce-method | GRangesList objects
reduce-method | Inter range transformations of a GenomicRanges object
renameSeqlevels | seqlevels utility functions
resize-method | SummarizedExperiment instances
resize-method | Intra range transformations of a GenomicRanges object
restoreSeqlevels | seqlevels utility functions
restrict-method | GRangesList objects
restrict-method | SummarizedExperiment instances
restrict-method | Intra range transformations of a GenomicRanges object
rglist | GAlignments objects
rglist-method | GAlignments objects
rglist-method | GAlignmentsList objects
right | GAlignmentPairs objects
right-method | GAlignmentPairs objects
rname | GAlignments objects
rname-method | GAlignments objects
rname-method | GAlignmentsList objects
rname<- | GAlignments objects
rname<--method | GAlignments objects
rname<--method | GAlignmentsList objects
rowData | SummarizedExperiment instances
rowData-method | SummarizedExperiment instances
rowData<- | SummarizedExperiment instances
rowData<--method | SummarizedExperiment instances

## -- S --

score-method | GIntervalTree objects
score-method | GRanges objects
score-method | GRangesList objects
selectEncodingWithCompatibleStrand | encodeOverlaps method for GRangesList objects, and related utilities
Seqinfo | Seqinfo objects
seqinfo | Accessing/modifying sequence information
Seqinfo-class | Seqinfo objects
seqinfo-method | GAlignmentPairs objects
seqinfo-method | GAlignments objects
seqinfo-method | GAlignmentsList objects
seqinfo-method | GIntervalTree objects
seqinfo-method | GRanges objects
seqinfo-method | GRangesList objects
seqinfo-method | SummarizedExperiment instances
seqinfo-method | Accessing/modifying sequence information
seqinfo<- | Accessing/modifying sequence information
seqinfo<--method | GAlignmentPairs objects
seqinfo<--method | GAlignments objects
seqinfo<--method | GAlignmentsList objects
seqinfo<--method | GRanges objects
seqinfo<--method | GRangesList objects
seqinfo<--method | SummarizedExperiment instances
seqinfo<--method | Accessing/modifying sequence information
seqlengths | Accessing/modifying sequence information
seqlengths-method | Seqinfo objects
seqlengths-method | Accessing/modifying sequence information
seqlengths<- | Accessing/modifying sequence information
seqlengths<--method | Seqinfo objects
seqlengths<--method | Accessing/modifying sequence information
seqlevels | Accessing/modifying sequence information
seqlevels-method | Seqinfo objects
seqlevels-method | Accessing/modifying sequence information
seqlevels-utils | seqlevels utility functions
seqlevels0 | Accessing/modifying sequence information
seqlevels<- | Accessing/modifying sequence information
seqlevels<--method | Seqinfo objects
seqlevels<--method | Accessing/modifying sequence information
seqlevelsInUse | Accessing/modifying sequence information
seqlevelsInUse-method | GAlignmentPairs objects
seqlevelsInUse-method | SummarizedExperiment instances
seqlevelsInUse-method | Accessing/modifying sequence information
seqnames | Accessing/modifying sequence information
seqnames-method | GAlignmentPairs objects
seqnames-method | GAlignments objects
seqnames-method | GAlignmentsList objects
seqnames-method | GIntervalTree objects
seqnames-method | GRanges objects
seqnames-method | GRangesList objects
seqnames-method | Seqinfo objects
seqnames-method | SummarizedExperiment instances
seqnames-method | Accessing/modifying sequence information
seqnames<- | Accessing/modifying sequence information
seqnames<--method | GAlignments objects
seqnames<--method | GAlignmentsList objects
seqnames<--method | GRanges objects
seqnames<--method | GRangesList objects
seqnames<--method | Seqinfo objects
seqnameStyle | Accessing/modifying sequence information
seqnameStyle-method | Seqinfo objects
seqnameStyle-method | Accessing/modifying sequence information
seqnameStyle<- | Accessing/modifying sequence information
seqnameStyle<--method | Seqinfo objects
seqnameStyle<--method | Accessing/modifying sequence information
setdiff-method | Set operations on GRanges/GRangesList/GAlignments objects
setops-methods | Set operations on GRanges/GRangesList/GAlignments objects
shift-method | GRangesList objects
shift-method | SummarizedExperiment instances
shift-method | Intra range transformations of a GenomicRanges object
show-method | GAlignmentPairs objects
show-method | GAlignments objects
show-method | GAlignmentsList objects
show-method | GIntervalTree objects
show-method | GRanges objects
show-method | GRangesList objects
show-method | Seqinfo objects
show-method | SummarizedExperiment instances
SimpleGenomicRangesList-class | GenomicRangesList objects
sort-method | SummarizedExperiment instances
sortSeqlevels | Accessing/modifying sequence information
sortSeqlevels-method | Accessing/modifying sequence information
split-method | SummarizedExperiment instances
splitAsListReturnedClass,GRange | GRanges objects
splitAsListReturnedClass-method | GAlignments objects
splitAsListReturnedClass-method | GRanges objects
splitAsListReturnedClass-method | SummarizedExperiment instances
splitCigar | CIGAR utility functions
start-method | GAlignments objects
start-method | GAlignmentsList objects
start-method | GIntervalTree 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 | GAlignmentPairs objects
strand-method | GAlignments objects
strand-method | GAlignmentsList objects
strand-method | GIntervalTree objects
strand-method | GRanges objects
strand-method | GRangesList objects
strand-method | SummarizedExperiment instances
strand-method | Strand utilities
strand-utils | Strand utilities
strand<--method | GAlignmentPairs objects
strand<--method | GAlignments objects
strand<--method | GAlignmentsList objects
strand<--method | GRanges objects
strand<--method | GRangesList objects
strand<--method | SummarizedExperiment instances
strand<--method | Strand utilities
subsetByOverlaps-method | SummarizedExperiment instances
subsetByOverlaps-method | Finding overlapping genomic ranges
summarizeCigarTable | CIGAR utility functions
SummarizedExperiment | SummarizedExperiment instances
SummarizedExperiment-class | SummarizedExperiment instances
SummarizedExperiment-method | SummarizedExperiment instances
summarizeOverlaps | Perform overlap queries between reads and genomic features
summarizeOverlaps-method | Perform overlap queries between reads and genomic features

## -- T --

tileGenome | Put (virtual) tiles on a given genome
trim-method | Intra range transformations of a GenomicRanges object

## -- U --

Union | Perform overlap queries between reads and genomic features
union-method | Set operations on GRanges/GRangesList/GAlignments objects
unlist-method | GAlignmentPairs objects
updateObject-method | GAlignments objects
updateObject-method | GAlignmentsList objects
updateObject-method | GRanges objects
updateObject-method | GRangesList objects
updateObject-method | Seqinfo objects
updateObject-method | SummarizedExperiment instances

## -- V --

validCigar | CIGAR utility functions
values-method | SummarizedExperiment instances
values<--method | SummarizedExperiment instances

## -- W --

width-method | GAlignments objects
width-method | GAlignmentsList objects
width-method | GIntervalTree 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
%in%-method | Comparing and ordering genomic ranges
%in%-method | SummarizedExperiment instances
%in%-method | Finding overlapping genomic ranges
<=-method | Comparing and ordering genomic ranges
==-method | Comparing and ordering genomic ranges
[-method | GIntervalTree objects
[-method | GRanges objects
[-method | GRangesList objects
[-method | Seqinfo objects
[-method | SummarizedExperiment instances
[<--method | GRanges objects
[<--method | GRangesList objects
[<--method | SummarizedExperiment instances
[[-method | GAlignmentPairs objects
[[-method | SummarizedExperiment instances
[[<--method | GRangesList objects
[[<--method | SummarizedExperiment instances