Representation and manipulation of genomic intervals

Documentation for package ‘GenomicRanges’ version 1.16.4

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

-- A --

as.data.frame-method	GRanges objects
as.data.frame-method	GRangesList 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-class	SummarizedExperiment instances
assays-method	SummarizedExperiment instances
assays<-	SummarizedExperiment instances
assays<--method	SummarizedExperiment instances

-- 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:GenomicRanges	GRanges objects
class:GenomicRangesList	GenomicRangesList objects
class:GIntervalTree	GIntervalTree objects
class:GRanges	GRanges objects
class:GRangesList	GRangesList objects
class:Seqinfo	Seqinfo objects
class:SimpleGenomicRangesList	GenomicRangesList objects
coerce-method	GIntervalTree objects
coerce-method	GRanges objects
coerce-method	GRangesList objects
coerce-method	GenomicRangesList objects
coerce-method	Seqinfo objects
coerce-method	Make a GRanges object from a data.frame or DataFrame
coerce-method	Mapping ranges between sequences
colData	SummarizedExperiment instances
colData-method	SummarizedExperiment instances
colData<-	SummarizedExperiment instances
colData<--method	SummarizedExperiment instances
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 --

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-method	SummarizedExperiment instances
distance-method	Finding the nearest genomic range neighbor
distanceToNearest-method	SummarizedExperiment instances
distanceToNearest-method	Finding the nearest genomic range neighbor
dropSeqlevels	seqlevels utility functions
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	GRanges objects
elementMetadata<--method	GRangesList objects
elementMetadata<--method	SummarizedExperiment instances
end-method	GIntervalTree 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-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
genome	Accessing/modifying sequence information
genome-method	Seqinfo objects
genome-method	Accessing/modifying sequence information
genome<-	Accessing/modifying sequence information
genome<--method	Seqinfo objects
genome<--method	Accessing/modifying sequence information
GenomicRanges	GRanges objects
GenomicRanges-class	GRanges objects
GenomicRanges-comparison	Comparing and ordering genomic ranges
GenomicRanges-deprecated	Deprecated Functions in package 'GenomicRanges'
GenomicRangesList	GenomicRangesList objects
GenomicRangesList-class	GenomicRangesList objects
GenomicRangesORGRangesList-class	GRanges objects
GenomicRangesORmissing-class	GRanges objects
GIntervalTree	GIntervalTree objects
GIntervalTree-class	GIntervalTree objects
GRanges	GRanges objects
granges	Squeeze the ranges out of a range-based object
GRanges-class	GRanges objects
granges-method	SummarizedExperiment instances
granges-method	Mapping ranges between sequences
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	Seqinfo objects
intersect-method	Set operations on GRanges and GRangesList objects
intra-range-methods	Intra range transformations of a GRanges or GRangesList object
isCircular	Accessing/modifying sequence information
isCircular-method	Seqinfo objects
isCircular-method	Accessing/modifying sequence information
isCircular<-	Accessing/modifying sequence information
isCircular<--method	Seqinfo objects
isCircular<--method	Accessing/modifying sequence information
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

-- K --

keepSeqlevels	seqlevels utility functions
keepStandardChromosomes	seqlevels utility functions

-- L --

length-method	GRanges objects
length-method	Seqinfo objects

-- M --

makeGRangesFromDataFrame	Make a GRanges object from a data.frame or DataFrame
makeGRangesListFromFeatureFragments	GRangesList objects
makeSeqnameIds	Deprecated Functions in package 'GenomicRanges'
map-method	Mapping ranges between sequences
match-method	Comparing and ordering genomic ranges
mcols-method	SummarizedExperiment instances
mcols<--method	SummarizedExperiment instances
merge-method	Seqinfo objects

-- N --

names-method	GIntervalTree objects
names-method	GRanges objects
names-method	Seqinfo objects
names<--method	GRanges objects
names<--method	Seqinfo 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-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-method	Set operations on GRanges and GRangesList objects
phicoef	Calculate the "phi coefficient" between two binary variables
pintersect-method	Set operations on GRanges and GRangesList objects
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-method	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	GIntervalTree 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
relistToClass-method	GRangesList objects
renameSeqlevels	seqlevels utility functions
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
restoreSeqlevels	seqlevels utility functions
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-method	SummarizedExperiment instances
rowData<-	SummarizedExperiment instances
rowData<--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	Seqinfo objects
seqinfo	Accessing/modifying sequence information
Seqinfo-class	Seqinfo objects
seqinfo-method	GIntervalTree objects
seqinfo-method	GRanges objects
seqinfo-method	GRangesList objects
seqinfo-method	SummarizedExperiment instances
seqinfo-method	Accessing/modifying sequence information
seqinfo<-	Accessing/modifying sequence information
seqinfo<--method	GRanges objects
seqinfo<--method	GRangesList objects
seqinfo<--method	SummarizedExperiment instances
seqinfo<--method	Accessing/modifying sequence information
seqlengths	Accessing/modifying sequence information
seqlengths-method	Seqinfo objects
seqlengths-method	Accessing/modifying sequence information
seqlengths<-	Accessing/modifying sequence information
seqlengths<--method	Seqinfo objects
seqlengths<--method	Accessing/modifying sequence information
seqlevels	Accessing/modifying sequence information
seqlevels-method	Seqinfo objects
seqlevels-method	Accessing/modifying sequence information
seqlevels-utils	seqlevels utility functions
seqlevels0	Accessing/modifying sequence information
seqlevels<-	Accessing/modifying sequence information
seqlevels<--method	Seqinfo objects
seqlevels<--method	Accessing/modifying sequence information
seqlevelsInUse	Accessing/modifying sequence information
seqlevelsInUse-method	SummarizedExperiment instances
seqlevelsInUse-method	Accessing/modifying sequence information
seqlevelsStyle-method	Accessing/modifying sequence information
seqlevelsStyle<--method	Accessing/modifying sequence information
seqnames	Accessing/modifying sequence information
seqnames-method	GIntervalTree objects
seqnames-method	GRanges objects
seqnames-method	GRangesList objects
seqnames-method	Seqinfo objects
seqnames-method	SummarizedExperiment instances
seqnames-method	Accessing/modifying sequence information
seqnames<-	Accessing/modifying sequence information
seqnames<--method	GRanges objects
seqnames<--method	GRangesList objects
seqnames<--method	Seqinfo objects
seqnameStyle	Accessing/modifying sequence information
seqnameStyle-method	Accessing/modifying sequence information
seqnameStyle<-	Accessing/modifying sequence information
seqnameStyle<--method	Accessing/modifying sequence information
setdiff-method	Set operations on GRanges and GRangesList objects
setops-methods	Set operations on GRanges and GRangesList objects
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	Seqinfo 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
sortSeqlevels	Accessing/modifying sequence information
sortSeqlevels-method	Accessing/modifying sequence information
split-method	SummarizedExperiment instances
splitAsListReturnedClass-method	GRangesList objects
start-method	GIntervalTree 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	GIntervalTree 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 --

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-method	Set operations on GRanges and GRangesList objects
updateObject-method	GRanges objects
updateObject-method	GRangesList objects
updateObject-method	Seqinfo objects
updateObject-method	SummarizedExperiment instances

-- V --

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

-- W --

width-method	GIntervalTree 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	Comparing and ordering genomic ranges
==-method	Comparing and ordering genomic ranges
[-method	GIntervalTree objects
[-method	GRanges objects
[-method	GRangesList objects
[-method	Seqinfo objects
[-method	SummarizedExperiment instances
[<--method	GRanges objects
[<--method	GRangesList objects
[<--method	SummarizedExperiment instances
[[-method	SummarizedExperiment instances
[[<--method	GRangesList objects
[[<--method	SummarizedExperiment instances