# Representation and manipulation of genomic intervals

## Documentation for package ‘GenomicRanges’ version 1.2.3

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

## Help Pages

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

## -- --

%in%-method | GappedAlignments objects
%in%-method | GRanges and GRangesList Interval Overlaps

## -- 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
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:GRanges | GRanges objects
class:GRangesList | GRangesList objects
class:Seqinfo | Seqinfo objects
coerce-method | GRanges objects
coerce-method | GRangesList objects
colData | SummarizedExperiment instances
colData-method | SummarizedExperiment instances
colData<- | SummarizedExperiment instances
colData<--method | SummarizedExperiment instances
countOverlaps-method | GappedAlignments objects
countOverlaps-method | GRanges and GRangesList Interval Overlaps
coverage-method | GRanges objects
coverage-method | GRangesList objects
coverage-method | GappedAlignments objects

## -- D --

dim-method | SummarizedExperiment instances
dimnames-method | SummarizedExperiment instances
dimnames<--method | SummarizedExperiment instances
disjoin-method | GRanges objects

## -- E --

elementMetadata-method | GRanges objects
elementMetadata-method | GRangesList 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 | GappedAlignments objects
findOverlaps-method | GRanges and GRangesList Interval Overlaps
flank-method | GRanges objects

## -- G --

GappedAlignments | GappedAlignments objects
GappedAlignments-class | GappedAlignments objects
gaps-method | GRanges objects
GenomicRanges | GRanges objects
GenomicRanges-class | GRanges objects
GRanges | GRanges objects
GRanges-class | GRanges objects
GRanges-setops | GRanges and GRangesList Set and Parallel Set Operations
GRangesList | GRangesList objects
GRangesList-class | GRangesList objects
grg | GappedAlignments objects
grg-method | GappedAlignments objects
grglist | GappedAlignments objects
grglist-method | GappedAlignments objects

## -- I --

intersect-method | GRanges and GRangesList Set and Parallel Set Operations
isCircular | Seqinfo objects
isCircular-method | GRanges objects
isCircular-method | GRangesList objects
isCircular-method | Seqinfo objects
isCircular<- | Seqinfo objects
isCircular<--method | Seqinfo objects
isCircularWithKnownLength | Seqinfo objects
isCircularWithKnownLength-method | GRanges objects
isCircularWithKnownLength-method | GRangesList objects
isCircularWithKnownLength-method | Seqinfo objects

## -- L --

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

## -- M --

match-method | GappedAlignments objects
match-method | GRanges and GRangesList Interval Overlaps

## -- N --

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

## -- P --

pintersect-method | GRanges and GRangesList Set and Parallel Set Operations
pintersect-method | GappedAlignments objects
psetdiff-method | GRanges and GRangesList Set and Parallel Set Operations
punion-method | GRanges and GRangesList Set and Parallel Set Operations

## -- 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
ranges-method | GRanges objects
ranges-method | GRangesList objects
ranges<--method | GRanges objects
ranges<--method | GRangesList objects
readGappedAlignments | GappedAlignments objects
reduce-method | GRanges objects
reduce-method | GRangesList objects
resize-method | GRanges objects
rev-method | GRanges 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 | GRanges objects
Seqinfo-class | Seqinfo objects
seqinfo-method | GRanges objects
seqinfo-method | GRangesList objects
seqlengths | Accessing the sequence names and lengths stored in an object
seqlengths-method | GRanges objects
seqlengths-method | GRangesList objects
seqlengths-method | GappedAlignments objects
seqlengths-method | Seqinfo objects
seqlengths<- | Accessing the sequence names and lengths stored in an object
seqlengths<--method | GRanges objects
seqlengths<--method | GRangesList objects
seqlengths<--method | GappedAlignments objects
seqlengths<--method | Seqinfo objects
seqnames | Accessing the sequence names and lengths stored in an object
seqnames-method | GRanges objects
seqnames-method | GRangesList objects
seqnames-method | GappedAlignments objects
seqnames-method | Seqinfo objects
seqnames<- | Accessing the sequence names and lengths stored in an object
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 | GRanges and GRangesList Set and Parallel Set Operations
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
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
subsetByOverlaps-method | GappedAlignments objects
subsetByOverlaps-method | GRanges and GRangesList Interval Overlaps
summarizeCigarTable | CIGAR utility functions
SummarizedExperiment | SummarizedExperiment instances
SummarizedExperiment-class | SummarizedExperiment instances
SummarizedExperiment-method | SummarizedExperiment instances

## -- U --

union-method | GRanges and GRangesList Set and Parallel Set Operations
unlist-method | GRangesList objects
updateObject-method | GRanges objects
updateObject-method | GRangesList 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 --

[-method | GRanges objects
[-method | GRangesList objects
[-method | GappedAlignments objects
[-method | SummarizedExperiment instances
[<--method | GRanges objects
[<--method | GRangesList objects
[<--method | SummarizedExperiment instances
[[<--method | GRangesList objects