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

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