Representation and manipulation of genomic intervals


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Documentation for package ‘GenomicRanges’ version 1.46.1

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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-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-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
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 --

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