R: Representation and manipulation of genomic intervals

# Representation and manipulation of genomic intervals

## Documentation for package ‘GenomicRanges’ version 1.56.1

- 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 | Memory-efficient representation of genomic positions
as.data.frame-method | GRanges objects
as.data.frame.GPos | Memory-efficient representation of genomic positions
as.factor-method | GRanges objects

## -- B --

bindAsGRanges | Manipulating genomic variables
bindROWS-method | GRanges objects
binnedAverage | Manipulating genomic variables

## -- C --

checkConstraint | Enforcing constraints thru Constraint objects
class:CompressedGenomicRangesList | GenomicRangesList objects
class:CompressedGRangesList | GRangesList objects
class:Constraint | Enforcing constraints thru Constraint objects
class:Constraint_OR_NULL | Enforcing constraints thru Constraint objects
class:DelegatingGenomicRanges | DelegatingGenomicRanges objects
class:GenomicPos | GRanges objects
class:GenomicRanges | GRanges objects
class:GenomicRangesList | GenomicRangesList objects
class:GenomicRanges_OR_GenomicRangesList | GenomicRangesList objects
class:GenomicRanges_OR_GRangesList | GRangesList objects
class:GNCList | GNCList objects
class:GPos | Memory-efficient representation of genomic positions
class:GRanges | GRanges objects
class:GRangesFactor | GRangesFactor objects
class:GRangesList | GRangesList objects
class:IRanges_OR_IPos | GRanges objects
class:SimpleGenomicRangesList | GenomicRangesList objects
class:SimpleGRangesList | GRangesList objects
class:StitchedGPos | Memory-efficient representation of genomic positions
class:UnstitchedGPos | Memory-efficient representation of genomic positions
coerce-method | GNCList objects
coerce-method | Memory-efficient representation of genomic positions
coerce-method | GRanges objects
coerce-method | GRangesFactor objects
coerce-method | GRangesList objects
coerce-method | Manipulating genomic variables
coerce-method | Make a GRanges object from a data.frame or DataFrame
CompressedGenomicRangesList | GenomicRangesList objects
CompressedGenomicRangesList-class | GenomicRangesList objects
CompressedGRangesList | GRangesList objects
CompressedGRangesList-class | GRangesList objects
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/position neighbor
distance-method | Finding the nearest genomic range/position neighbor
distanceToNearest | Finding the nearest genomic range/position neighbor
distanceToNearest-method | Finding the nearest genomic range/position neighbor
duplicated-method | Comparing and ordering genomic ranges
duplicated.GenomicRanges | Comparing and ordering genomic ranges

## -- E --

elementMetadata-method | GenomicRangesList objects
elementMetadata<--method | GenomicRangesList objects
end-method | GNCList objects
end-method | GRangesFactor objects
end<--method | GRanges objects
end<--method | GenomicRangesList objects
extractROWS-method | GenomicRangesList objects

## -- F --

FactorToClass-method | GRangesFactor objects
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/position neighbor
follow-method | Finding the nearest genomic range/position neighbor
from_GPos_to_GRanges | Memory-efficient representation of genomic positions

## -- G --

gaps | Inter range transformations of a GRanges or GRangesList object
gaps-method | Inter range transformations of a GRanges or GRangesList object
genomic-range-squeezers | Squeeze the genomic ranges out of a range-based object
GenomicPos | GRanges objects
GenomicPos-class | GRanges objects
GenomicRanges | GRanges objects
GenomicRanges-class | GRanges objects
GenomicRanges-comparison | Comparing and ordering genomic ranges
GenomicRangesList | GenomicRangesList objects
GenomicRangesList-class | GenomicRangesList objects
GenomicRanges_OR_GenomicRangesList | GenomicRangesList objects
GenomicRanges_OR_GenomicRangesList-class | GenomicRangesList objects
GenomicRanges_OR_GRangesList | GRangesList objects
GenomicRanges_OR_GRangesList-class | GRangesList objects
GenomicRanges_OR_missing-class | GRanges objects
genomicvariables | Manipulating genomic variables
genomicvars | Manipulating genomic variables
getListElement-method | GRanges objects
getListElement-method | GenomicRangesList objects
GNCList | GNCList objects
GNCList-class | GNCList objects
GPos | Memory-efficient representation of genomic positions
GPos-class | Memory-efficient representation of genomic positions
GRanges | GRanges objects
granges | Squeeze the genomic ranges out of a range-based object
GRanges-class | GRanges objects
granges-method | GNCList objects
granges-method | GRanges objects
granges-method | GRangesFactor objects
GRangesFactor | GRangesFactor objects
GRangesFactor-class | GRangesFactor objects
GRangesList | GRangesList objects
GRangesList-class | GRangesList objects
grglist | Squeeze the genomic ranges out of a range-based object
grglist-method | Squeeze the genomic 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
IRanges_OR_IPos | GRanges objects
IRanges_OR_IPos-class | GRanges objects
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 | GRanges objects
length-method | GenomicRangesList 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 | GRanges objects
names-method | GenomicRangesList objects
names<--method | GRanges objects
names<--method | GenomicRangesList 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/position neighbor
nearest-method | Finding the nearest genomic range/position neighbor
nearest-methods | Finding the nearest genomic range/position neighbor
nearestKNeighbors | Finding the nearest genomic range/position neighbor
nearestKNeighbors-method | Finding the nearest genomic range/position neighbor

## -- O --

order-method | Comparing and ordering genomic ranges
overlapsAny | Finding overlapping genomic ranges

## -- P --

parallel_slot_names-method | GRanges objects
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-method | Memory-efficient representation of genomic positions
pos-method | GRangesFactor objects
precede | Finding the nearest genomic range/position neighbor
precede-method | Finding the nearest genomic range/position 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
ranges-method | DelegatingGenomicRanges objects
ranges-method | GNCList objects
ranges-method | GRanges objects
ranges-method | GRangesFactor 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

## -- S --

score-method | GRanges objects
score-method | GenomicRangesList objects
score<--method | GRanges objects
score<--method | GenomicRangesList objects
selfmatch-method | Comparing and ordering genomic ranges
seqinfo-method | DelegatingGenomicRanges objects
seqinfo-method | GNCList objects
seqinfo-method | GRanges objects
seqinfo-method | GRangesFactor objects
seqinfo-method | GenomicRangesList objects
seqinfo<--method | GRanges objects
seqinfo<--method | GenomicRangesList objects
seqnames-method | DelegatingGenomicRanges objects
seqnames-method | GNCList objects
seqnames-method | GRanges objects
seqnames-method | GRangesFactor objects
seqnames-method | GenomicRangesList objects
seqnames<--method | GRanges objects
seqnames<--method | GenomicRangesList 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 | Memory-efficient representation of genomic positions
show-method | GRanges objects
show-method | GRangesFactor objects
show-method | GenomicRangesList objects
SimpleGenomicRangesList | GenomicRangesList objects
SimpleGenomicRangesList-class | GenomicRangesList objects
SimpleGRangesList | GRangesList objects
SimpleGRangesList-class | GRangesList objects
slidingWindows | Generate windows for a GenomicRanges
slidingWindows-method | Generate windows for a GenomicRanges
sort-method | GRangesList objects
sort-method | Comparing and ordering genomic ranges
sort.GenomicRanges | Comparing and ordering genomic ranges
sort.GRangesList | GRangesList objects
start-method | GNCList objects
start-method | GRanges objects
start-method | GRangesFactor objects
start<--method | GRanges objects
start<--method | GenomicRangesList objects
StitchedGPos | Memory-efficient representation of genomic positions
StitchedGPos-class | Memory-efficient representation of genomic positions
strand-method | DelegatingGenomicRanges objects
strand-method | GNCList objects
strand-method | GRanges objects
strand-method | GRangesFactor objects
strand-method | GenomicRangesList objects
strand-method | Strand utilities
strand-utils | Strand utilities
strand<--method | GRanges objects
strand<--method | GenomicRangesList objects
strand<--method | Strand utilities
subsetByOverlaps | Finding overlapping genomic ranges
subtract | Subtract a set of genomic ranges from a GRanges object
subtract-method | Subtract a set of genomic ranges from a GRanges object
subtract-methods | Subtract a set of genomic ranges from a GRanges object
summary-method | Memory-efficient representation of genomic positions
summary-method | GRanges objects
summary.GenomicRanges | GRanges objects
summary.GPos | Memory-efficient representation of genomic positions

## -- T --

terminators | Intra range transformations of a GRanges or GRangesList object
terminators-method | Intra range transformations of a GRanges or GRangesList object
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 | Intra range transformations of a GRanges or GRangesList object
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
unlist-method | GenomicRangesList objects
UnstitchedGPos | Memory-efficient representation of genomic positions
UnstitchedGPos-class | Memory-efficient representation of genomic positions
update-method | DelegatingGenomicRanges objects
update-method | GRanges objects
updateObject-method | Memory-efficient representation of genomic positions
updateObject-method | GRanges objects
updateObject-method | GenomicRangesList objects
update_ranges-method | Intra range transformations of a GRanges or GRangesList object

## -- W --

width-method | GNCList objects
width-method | GRanges objects
width-method | GRangesFactor objects
width<--method | GRanges objects
width<--method | GenomicRangesList objects

## -- misc --

$-method | GRanges objects
$<--method | GRanges objects
[-method | GRanges objects
[-method | GRangesList objects
[<--method | GRangesList objects