Representation and manipulation of genomic intervals and variables defined along a genome


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Documentation for package ‘GenomicRanges’ version 1.22.4

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

-- A --

absoluteRanges Transform genomic ranges into "absolute" ranges
as.character-method GRanges objects
as.data.frame-method GRanges objects
as.factor-method GRanges objects
assay SummarizedExperiment instances
assay-method SummarizedExperiment instances
assay<- SummarizedExperiment instances
assay<--method SummarizedExperiment instances
assayNames SummarizedExperiment instances
assayNames-method SummarizedExperiment instances
assayNames<- SummarizedExperiment instances
assayNames<--method SummarizedExperiment instances
assays SummarizedExperiment instances
Assays-class SummarizedExperiment instances
assays-method SummarizedExperiment instances
assays<- SummarizedExperiment instances
assays<--method SummarizedExperiment instances

-- B --

bindAsGRanges Manipulating genomic variables
binnedAverage Manipulating genomic variables

-- C --

c-method GRanges objects
cbind-method SummarizedExperiment instances
checkConstraint Enforcing constraints thru Constraint objects
class:Constraint Enforcing constraints thru Constraint objects
class:ConstraintORNULL Enforcing constraints thru Constraint objects
class:DelegatingGenomicRanges DelegatingGenomicRanges objects
class:GenomicRanges GRanges objects
class:GenomicRangesList GenomicRangesList objects
class:GIntervalTree GIntervalTree objects
class:GNCList GNCList objects
class:GRanges GRanges objects
class:GRangesList GRangesList objects
class:SimpleGenomicRangesList GenomicRangesList objects
coerce-method GIntervalTree objects
coerce-method GNCList objects
coerce-method GRanges objects
coerce-method GRangesList objects
coerce-method GenomicRangesList objects
coerce-method SummarizedExperiment instances
coerce-method Manipulating genomic variables
coerce-method Make a GRanges object from a data.frame or DataFrame
colData SummarizedExperiment instances
colData-method SummarizedExperiment instances
colData<- SummarizedExperiment instances
colData<--method SummarizedExperiment instances
compare Comparing and ordering genomic ranges
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
countOverlaps Finding overlapping genomic ranges
countOverlaps-method SummarizedExperiment instances
countOverlaps-method Finding overlapping genomic ranges
coverage Coverage of a GRanges or GRangesList object
coverage-method SummarizedExperiment instances
coverage-method Coverage of a GRanges or GRangesList object
coverage-methods Coverage of a GRanges or GRangesList object

-- D --

DelegatingGenomicRanges-class DelegatingGenomicRanges objects
dim-method SummarizedExperiment instances
dimnames-method SummarizedExperiment instances
dimnames<--method SummarizedExperiment instances
disjoin Inter range transformations of a GenomicRanges or GRangesList object
disjoin-method Inter range transformations of a GenomicRanges or GRangesList object
disjointBins Inter range transformations of a GenomicRanges or GRangesList object
disjointBins-method SummarizedExperiment instances
disjointBins-method Inter range transformations of a GenomicRanges or GRangesList object
distance Finding the nearest genomic range neighbor
distance-method SummarizedExperiment instances
distance-method Finding the nearest genomic range neighbor
distanceToNearest Finding the nearest genomic range neighbor
distanceToNearest-method SummarizedExperiment instances
distanceToNearest-method Finding the nearest genomic range neighbor
duplicated-method Comparing and ordering genomic ranges
duplicated-method SummarizedExperiment instances
duplicated.GenomicRanges Comparing and ordering genomic ranges

-- E --

elementMetadata-method GIntervalTree objects
elementMetadata-method GRangesList objects
elementMetadata-method SummarizedExperiment instances
elementMetadata<--method GRangesList objects
elementMetadata<--method SummarizedExperiment instances
end-method GIntervalTree objects
end-method GNCList 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
exptData SummarizedExperiment instances
exptData-method SummarizedExperiment instances
exptData<- SummarizedExperiment instances
exptData<--method SummarizedExperiment instances

-- F --

findOverlaps Finding overlapping genomic ranges
findOverlaps-method SummarizedExperiment instances
findOverlaps-method Finding overlapping genomic ranges
findOverlaps-methods Finding overlapping genomic ranges
flank Intra range transformations of a GRanges or GRangesList object
flank-method SummarizedExperiment instances
flank-method Intra range transformations of a GRanges or GRangesList object
follow Finding the nearest genomic range neighbor
follow-method SummarizedExperiment instances
follow-method Finding the nearest genomic range neighbor

-- G --

gaps Inter range transformations of a GenomicRanges or GRangesList object
gaps-method Inter range transformations of a GenomicRanges or GRangesList object
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
genomicvariables Manipulating genomic variables
genomicvars Manipulating genomic variables
GIntervalTree GIntervalTree objects
GIntervalTree-class GIntervalTree objects
GNCList GNCList objects
GNCList-class GNCList objects
GRanges GRanges objects
granges Squeeze the ranges out of a range-based object
GRanges-class GRanges objects
granges-method GNCList objects
granges-method GRanges objects
granges-method SummarizedExperiment instances
GRangesList GRangesList objects
GRangesList-class GRangesList objects
grglist Squeeze the ranges out of a range-based object

-- I --

inter-range-methods Inter range transformations of a GenomicRanges or GRangesList object
intersect-method Set operations on GRanges and GRangesList objects
intra-range-methods Intra range transformations of a GRanges or GRangesList object
is.unsorted-method Comparing and ordering genomic ranges
isDisjoint Inter range transformations of a GenomicRanges or GRangesList object
isDisjoint-method SummarizedExperiment instances
isDisjoint-method Inter range transformations of a GenomicRanges or GRangesList object
isSmallGenome Transform genomic ranges into "absolute" ranges

-- L --

length-method GNCList objects
length-method GRanges objects

-- M --

makeGRangesFromDataFrame Make a GRanges object from a data.frame or DataFrame
makeGRangesListFromFeatureFragments GRangesList objects
makeSummarizedExperimentFromExpressionSet Make a SummarizedExperiment object from an ExpressionSet
mapCoords Mapping ranges between sequences
mapCoords-method Mapping ranges between sequences
mapCoords-methods Mapping ranges between sequences
match-method Comparing and ordering genomic ranges
mcolAsRleList Manipulating genomic variables
mcols-method SummarizedExperiment instances
mcols<--method SummarizedExperiment instances

-- N --

names-method GIntervalTree objects
names-method GNCList objects
names-method GRanges objects
names<--method GRanges objects
narrow Intra range transformations of a GRanges or GRangesList object
narrow-method SummarizedExperiment instances
narrow-method Intra range transformations of a GRanges or GRangesList object
nearest Finding the nearest genomic range neighbor
nearest-method SummarizedExperiment instances
nearest-method Finding the nearest genomic range neighbor
nearest-methods Finding the nearest genomic range neighbor

-- O --

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

-- P --

pgap Set operations on GRanges and GRangesList objects
pgap-method Set operations on GRanges and GRangesList objects
phicoef Calculate the "phi coefficient" between two binary variables
pintersect Set operations on GRanges and GRangesList objects
pintersect-method Set operations on GRanges and GRangesList objects
pmapCoords Mapping ranges between sequences
pmapCoords-method Mapping ranges between sequences
precede Finding the nearest genomic range neighbor
precede-method SummarizedExperiment instances
precede-method Finding the nearest genomic range 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 GRanges and GRangesList objects
psetdiff-method Set operations on GRanges and GRangesList objects
punion Set operations on GRanges and GRangesList objects
punion-method Set operations on GRanges and GRangesList objects

-- R --

range Inter range transformations of a GenomicRanges or GRangesList object
range-method Inter range transformations of a GenomicRanges or GRangesList object
range-squeezers Squeeze the ranges out of a range-based object
ranges-method DelegatingGenomicRanges objects
ranges-method GIntervalTree objects
ranges-method GNCList 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
reduce Inter range transformations of a GenomicRanges or GRangesList object
reduce-method Inter range transformations of a GenomicRanges 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 SummarizedExperiment instances
resize-method Intra range transformations of a GRanges or GRangesList object
restrict Intra range transformations of a GRanges or GRangesList object
restrict-method SummarizedExperiment instances
restrict-method Intra range transformations of a GRanges or GRangesList object
rglist Squeeze the ranges out of a range-based object
rowData SummarizedExperiment instances
rowData<- SummarizedExperiment instances
rowRanges SummarizedExperiment instances
rowRanges-method SummarizedExperiment instances
rowRanges<- SummarizedExperiment instances
rowRanges<--method SummarizedExperiment instances

-- S --

score-method GIntervalTree objects
score-method GRanges objects
score-method GRangesList objects
score<--method GRanges objects
score<--method GRangesList objects
seqinfo-method DelegatingGenomicRanges objects
seqinfo-method GIntervalTree objects
seqinfo-method GNCList objects
seqinfo-method GRanges objects
seqinfo-method GRangesList objects
seqinfo-method SummarizedExperiment instances
seqinfo<--method GRanges objects
seqinfo<--method GRangesList objects
seqinfo<--method SummarizedExperiment instances
seqnames-method DelegatingGenomicRanges objects
seqnames-method GIntervalTree objects
seqnames-method GNCList objects
seqnames-method GRanges objects
seqnames-method GRangesList objects
seqnames-method SummarizedExperiment instances
seqnames<--method GRanges objects
seqnames<--method GRangesList objects
setdiff-method Set operations on GRanges and GRangesList objects
setops-methods Set operations on GRanges and GRangesList objects
ShallowData-class SummarizedExperiment instances
ShallowSimpleListAssays-class SummarizedExperiment instances
shift Intra range transformations of a GRanges or GRangesList object
shift-method SummarizedExperiment instances
shift-method Intra range transformations of a GRanges or GRangesList object
show-method GIntervalTree objects
show-method GRanges objects
show-method GRangesList objects
show-method SummarizedExperiment instances
SimpleGenomicRangesList-class GenomicRangesList objects
sort-method Comparing and ordering genomic ranges
sort-method SummarizedExperiment instances
sort.GenomicRanges Comparing and ordering genomic ranges
split-method SummarizedExperiment instances
start-method GIntervalTree objects
start-method GNCList 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 DelegatingGenomicRanges objects
strand-method GIntervalTree objects
strand-method GNCList objects
strand-method GRanges objects
strand-method GRangesList objects
strand-method SummarizedExperiment instances
strand-method Strand utilities
strand-utils Strand utilities
strand<--method GRanges objects
strand<--method GRangesList objects
strand<--method SummarizedExperiment instances
strand<--method Strand utilities
subset-method SummarizedExperiment instances
subsetByOverlaps Finding overlapping genomic ranges
subsetByOverlaps-method SummarizedExperiment instances
subsetByOverlaps-method Finding overlapping genomic ranges
SummarizedExperiment SummarizedExperiment instances
SummarizedExperiment-class SummarizedExperiment instances
SummarizedExperiment-method SummarizedExperiment instances

-- T --

tile-method Tile a GenomicRanges object
tile-methods Tile a GenomicRanges object
tileGenome Put (virtual) tiles on a given genome
trim-method Intra range transformations of a GRanges or GRangesList object

-- U --

union-method Set operations on GRanges and GRangesList objects
update-method DelegatingGenomicRanges objects
updateObject-method GRanges objects
updateObject-method GRangesList objects
updateObject-method SummarizedExperiment instances

-- V --

values-method SummarizedExperiment instances
values<--method SummarizedExperiment instances

-- W --

width-method GIntervalTree objects
width-method GNCList 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
[-method GIntervalTree objects
[-method GRanges objects
[-method GRangesList objects
[-method SummarizedExperiment instances
[<--method GRanges objects
[<--method GRangesList objects
[<--method SummarizedExperiment instances
[[-method SummarizedExperiment instances
[[<--method GRangesList objects
[[<--method SummarizedExperiment instances