# Representation and manipulation of genomic intervals

## Documentation for package ‘GenomicRanges’ version 1.6.7

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

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

## -- A --

as.data.frame-method | GRanges objects
as.data.frame-method | GRangesList objects
as.data.frame-method | GappedAlignments 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-method | SummarizedExperiment instances
assays<- | SummarizedExperiment instances
assays<--method | SummarizedExperiment instances

## -- C --

c-method | GRanges objects
c-method | GappedAlignments objects
cigar | GappedAlignments objects
cigar-method | GappedAlignments objects
cigar-utils | CIGAR utility functions
cigarNarrow | CIGAR utility functions
cigarOpTable | CIGAR utility functions
cigarQNarrow | 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
class:GappedAlignments | GappedAlignments objects
class:GenomicRanges | GRanges objects
class:GenomicRangesList | GenomicRangesList objects
class:GRanges | GRanges objects
class:GRangesList | GRangesList objects
class:Seqinfo | Seqinfo objects
class:SimpleGenomicRangesList | GenomicRangesList objects
coerce-method | GRanges objects
coerce-method | GRangesList objects
coerce-method | GappedAlignments objects
coerce-method | Seqinfo objects
colData | SummarizedExperiment instances
colData-method | SummarizedExperiment instances
colData<- | SummarizedExperiment instances
colData<--method | SummarizedExperiment instances
countGenomicOverlaps | Count Read Hits in Genomic Features
countGenomicOverlaps-method | Count Read Hits in Genomic Features
countOverlaps-method | GRanges, GRangesList and GappedAlignments Interval Overlaps
coverage-method | GRanges, GRangesList and GappedAlignments coverage
coverage-methods | GRanges, GRangesList and GappedAlignments coverage

## -- D --

dim-method | SummarizedExperiment instances
dimnames-method | SummarizedExperiment instances
dimnames<--method | SummarizedExperiment instances
disjoin-method | GRanges objects
distance-method | GRanges objects
duplicated-method | Ordering and comparing genomic ranges

## -- E --

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

## -- F --

findOverlaps-method | GRanges, GRangesList and GappedAlignments Interval Overlaps
findOverlaps-methods | GRanges, GRangesList and GappedAlignments Interval Overlaps
flank-method | GRanges objects
flank-method | GRangesList objects
follow-method | GRanges objects

## -- G --

GappedAlignments | GappedAlignments objects
GappedAlignments-class | GappedAlignments objects
gaps-method | GRanges objects
genome | Accessing sequence information
genome-method | Seqinfo objects
genome-method | Accessing sequence information
genome<- | Accessing sequence information
genome<--method | Seqinfo objects
genome<--method | Accessing sequence information
GenomicRanges | GRanges objects
GenomicRanges-class | GRanges objects
GenomicRanges-comparison | Ordering and comparing genomic ranges
GenomicRangesList | GenomicRangesList objects
GenomicRangesList-class | GenomicRangesList objects
GenomicRangesORGRangesList-class | GRanges objects
GenomicRangesORmissing-class | GRanges objects
GRanges | GRanges objects
granges | GappedAlignments objects
GRanges-class | GRanges objects
granges-method | GappedAlignments objects
GRangesList | GRangesList objects
GRangesList-class | GRangesList objects
grg | GappedAlignments objects
grglist | GappedAlignments objects
grglist-method | GappedAlignments objects

## -- I --

intersect-method | Set operations on GRanges/GRangesList/GappedAlignments objects
IntersectionNotEmpty | Count reads that map to genomic features
IntersectionStrict | Count reads that map to genomic features
isCircular | Accessing sequence information
isCircular-method | Seqinfo objects
isCircular-method | Accessing sequence information
isCircular<- | Accessing sequence information
isCircular<--method | Seqinfo objects
isCircular<--method | Accessing sequence information
isCircularWithKnownLength | Accessing sequence information
isCircularWithKnownLength-method | Seqinfo objects
isCircularWithKnownLength-method | Accessing sequence information
isDisjoint-method | GRanges objects
isDisjoint-method | GRangesList objects

## -- K --

keepSeqlevels | seqlevels utility functions
keepSeqlevels-method | seqlevels utility functions

## -- L --

length-method | GRanges objects
length-method | GappedAlignments objects
length-method | Seqinfo objects

## -- M --

makeGRangesListFromFeatureFragments | GRangesList objects
match-method | GRanges, GRangesList and GappedAlignments Interval Overlaps
merge-method | Seqinfo objects

## -- N --

names-method | GRanges objects
names-method | GappedAlignments objects
names-method | Seqinfo objects
names<--method | GRanges objects
names<--method | GappedAlignments objects
names<--method | Seqinfo objects
narrow-method | GappedAlignments objects
ngap-method | GappedAlignments objects

## -- O --

order-method | Ordering and comparing genomic ranges

## -- P --

pgap-method | Set operations on GRanges/GRangesList/GappedAlignments objects
pintersect-method | Set operations on GRanges/GRangesList/GappedAlignments objects
precede-method | GRanges objects
psetdiff-method | Set operations on GRanges/GRangesList/GappedAlignments objects
punion-method | Set operations on GRanges/GRangesList/GappedAlignments objects

## -- Q --

qnarrow | GappedAlignments objects
qnarrow-method | GappedAlignments objects
queryLoc2refLoc | CIGAR utility functions
queryLocs2refLocs | CIGAR utility functions
qwidth | GappedAlignments objects
qwidth-method | GappedAlignments objects

## -- R --

range-method | GRanges objects
range-method | GRangesList objects
ranges-method | GRanges objects
ranges-method | GRangesList objects
ranges-method | GappedAlignments objects
ranges<--method | GRanges objects
ranges<--method | GRangesList objects
rank-method | Ordering and comparing genomic ranges
readGappedAlignments | GappedAlignments objects
reduce-method | GRanges objects
reduce-method | GRangesList objects
renameSeqlevels | seqlevels utility functions
renameSeqlevels-method | seqlevels utility functions
resize-method | GRanges objects
restrict-method | GRanges objects
restrict-method | GRangesList objects
rglist | GappedAlignments objects
rglist-method | GappedAlignments objects
rname | GappedAlignments objects
rname-method | GappedAlignments objects
rname<- | GappedAlignments objects
rname<--method | GappedAlignments objects
rowData | SummarizedExperiment instances
rowData-method | SummarizedExperiment instances
rowData<- | SummarizedExperiment instances
rowData<--method | SummarizedExperiment instances

## -- S --

Seqinfo | Seqinfo objects
seqinfo | Accessing sequence information
Seqinfo-class | Seqinfo objects
seqinfo-method | GRanges objects
seqinfo-method | GRangesList objects
seqinfo-method | GappedAlignments objects
seqinfo<- | Accessing sequence information
seqinfo<--method | GRanges objects
seqinfo<--method | GRangesList objects
seqinfo<--method | GappedAlignments objects
seqlengths | Accessing sequence information
seqlengths-method | Seqinfo objects
seqlengths-method | Accessing sequence information
seqlengths<- | Accessing sequence information
seqlengths<--method | Seqinfo objects
seqlengths<--method | Accessing sequence information
seqlevels | Accessing sequence information
seqlevels-method | Seqinfo objects
seqlevels-method | Accessing sequence information
seqlevels<- | Accessing sequence information
seqlevels<--method | Seqinfo objects
seqlevels<--method | Accessing sequence information
seqnames | Accessing sequence information
seqnames-method | GRanges objects
seqnames-method | GRangesList objects
seqnames-method | GappedAlignments objects
seqnames-method | Seqinfo objects
seqnames<- | Accessing sequence information
seqnames<--method | GRanges objects
seqnames<--method | GRangesList objects
seqnames<--method | GappedAlignments objects
seqnames<--method | Seqinfo objects
seqselect-method | GRanges objects
seqselect<--method | GRanges objects
setdiff-method | Set operations on GRanges/GRangesList/GappedAlignments objects
setops-methods | Set operations on GRanges/GRangesList/GappedAlignments objects
shift-method | GRanges objects
shift-method | GRangesList objects
show-method | GRanges objects
show-method | GRangesList objects
show-method | GappedAlignments objects
show-method | Seqinfo objects
show-method | SummarizedExperiment instances
SimpleGenomicRangesList-class | GenomicRangesList objects
sort-method | Ordering and comparing genomic ranges
split-method | GRanges objects
splitCigar | CIGAR utility functions
start-method | GRanges objects
start-method | GRangesList objects
start-method | GappedAlignments objects
start<--method | GRanges objects
start<--method | GRangesList objects
strand | Accessing strand information
strand-method | GRanges objects
strand-method | GRangesList objects
strand-method | GappedAlignments objects
strand-method | Accessing strand information
strand-methods | Accessing strand information
strand<- | Accessing strand information
strand<--method | GRanges objects
strand<--method | GRangesList objects
strand<--method | GappedAlignments objects
subsetByOverlaps-method | GRanges, GRangesList and GappedAlignments Interval Overlaps
summarizeCigarTable | CIGAR utility functions
SummarizedExperiment | SummarizedExperiment instances
SummarizedExperiment-class | SummarizedExperiment instances
SummarizedExperiment-method | SummarizedExperiment instances
summarizeOverlaps | Count reads that map to genomic features
summarizeOverlaps-method | Count reads that map to genomic features

## -- U --

Union | Count reads that map to genomic features
union-method | Set operations on GRanges/GRangesList/GappedAlignments objects
unique-method | Ordering and comparing genomic ranges
unlist-method | GRangesList objects
updateObject-method | GRanges objects
updateObject-method | GRangesList objects
updateObject-method | GappedAlignments objects
updateObject-method | Seqinfo objects

## -- V --

validCigar | CIGAR utility functions

## -- W --

width-method | GRanges objects
width-method | GRangesList objects
width-method | GappedAlignments objects
width<--method | GRanges objects
width<--method | GRangesList objects
window-method | GRanges objects

## -- misc --

%in%-method | GRanges, GRangesList and GappedAlignments Interval Overlaps
<-method | Ordering and comparing genomic ranges
<=-method | Ordering and comparing genomic ranges
==-method | Ordering and comparing genomic ranges
>-method | Ordering and comparing genomic ranges
>=-method | Ordering and comparing genomic ranges
[-method | GRanges objects
[-method | GRangesList objects
[-method | GappedAlignments objects
[-method | Seqinfo objects
[-method | SummarizedExperiment instances
[<--method | GRanges objects
[<--method | GRangesList objects
[<--method | SummarizedExperiment instances
[[<--method | GRangesList objects