Representation and manipulation of genomic intervals


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Documentation for package ‘GenomicRanges’ version 1.8.13

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

-- A --

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

-- C --

c-method GRanges objects
c-method GappedAlignments objects
checkConstraint Enforcing constraints thru Constraint objects
cigar GappedAlignments objects
cigar-method GappedAlignments objects
cigar-utils CIGAR utility functions
cigarNarrow CIGAR utility functions
cigarOpTable CIGAR utility functions
cigarQNarrow CIGAR utility functions
cigarToCigarTable CIGAR utility functions
cigarToIRanges CIGAR utility functions
cigarToIRangesListByAlignment CIGAR utility functions
cigarToIRangesListByRName CIGAR utility functions
cigarToQWidth CIGAR utility functions
cigarToRleList CIGAR utility functions
cigarToWidth CIGAR utility functions
class:Constraint Enforcing constraints thru Constraint objects
class:ConstraintORNULL Enforcing constraints thru Constraint objects
class:GappedAlignmentPairs GappedAlignmentPairs objects
class:GappedAlignments GappedAlignments objects
class:GenomicRanges GRanges objects
class:GenomicRangesList GenomicRangesList objects
class:GRanges GRanges objects
class:GRangesList GRangesList objects
class:Seqinfo Seqinfo objects
class:SimpleGenomicRangesList GenomicRangesList objects
coerce-method GRanges objects
coerce-method GRangesList objects
coerce-method GappedAlignmentPairs objects
coerce-method GappedAlignments objects
coerce-method GenomicRangesList objects
coerce-method Seqinfo objects
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
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
countGenomicOverlaps Count Read Hits in Genomic Features
countGenomicOverlaps-method Count Read Hits in Genomic Features
countOverlaps-method GRanges, GRangesList, GappedAlignments and GappedAlignmentPairs Interval Overlaps
coverage-method Coverage of a GRanges, GRangesList, GappedAlignments, or GappedAlignmentPairs object
coverage-methods Coverage of a GRanges, GRangesList, GappedAlignments, or GappedAlignmentPairs object

-- D --

dim-method SummarizedExperiment instances
dimnames-method SummarizedExperiment instances
dimnames<--method SummarizedExperiment instances
disjoin-method GRanges objects
disjointBins-method GRanges objects
distance-method GRanges objects
duplicated-method Comparing and ordering genomic ranges

-- E --

elementMetadata-method GRanges objects
elementMetadata-method GRangesList objects
elementMetadata-method GappedAlignmentPairs objects
elementMetadata-method GappedAlignments objects
elementMetadata<--method GRanges objects
elementMetadata<--method GRangesList objects
elementMetadata<--method GappedAlignmentPairs objects
elementMetadata<--method GappedAlignments objects
encodeOverlaps-method encodeOverlaps methods and related utilities
encodeOverlaps-methods encodeOverlaps methods and related utilities
end-method GRanges objects
end-method GRangesList objects
end-method GappedAlignments objects
end<--method GRanges objects
end<--method GRangesList objects
exptData SummarizedExperiment instances
exptData-method SummarizedExperiment instances
exptData<- SummarizedExperiment instances
exptData<--method SummarizedExperiment instances
extractSkippedExonRanks encodeOverlaps methods and related utilities
extractSkippedExonRanks-method encodeOverlaps methods and related utilities

-- F --

findOverlaps-method GRanges, GRangesList, GappedAlignments and GappedAlignmentPairs Interval Overlaps
findOverlaps-methods GRanges, GRangesList, GappedAlignments and GappedAlignmentPairs Interval Overlaps
first GappedAlignmentPairs objects
first-method GappedAlignmentPairs objects
flank-method GRanges objects
flank-method GRangesList objects
flipQuery encodeOverlaps methods and related utilities
follow-method GRanges objects

-- G --

GappedAlignmentPairs GappedAlignmentPairs objects
GappedAlignmentPairs-class GappedAlignmentPairs objects
GappedAlignments GappedAlignments objects
GappedAlignments-class GappedAlignments objects
gaps-method GRanges objects
genome Accessing sequence information
genome-method Seqinfo objects
genome-method Accessing sequence information
genome<- Accessing sequence information
genome<--method Seqinfo objects
genome<--method Accessing sequence information
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
GRanges GRanges objects
granges GappedAlignments objects
GRanges-class GRanges objects
granges-method GappedAlignments objects
granges-method Mapping ranges between sequences
GRangesList GRangesList objects
GRangesList-class GRangesList objects
grg GappedAlignments objects
grglist GappedAlignments objects
grglist-method GappedAlignmentPairs objects
grglist-method GappedAlignments objects

-- I --

intersect-method Set operations on GRanges/GRangesList/GappedAlignments objects
IntersectionNotEmpty Count reads that map to genomic features
IntersectionStrict Count reads that map to genomic features
isCircular Accessing sequence information
isCircular-method Seqinfo objects
isCircular-method Accessing sequence information
isCircular<- Accessing sequence information
isCircular<--method Seqinfo objects
isCircular<--method Accessing sequence information
isCompatibleWithSkippedExons encodeOverlaps methods and related utilities
isCompatibleWithSkippedExons-method encodeOverlaps methods and related utilities
isCompatibleWithSplicing encodeOverlaps methods and related utilities
isCompatibleWithSplicing-method encodeOverlaps methods and related utilities
isDisjoint-method GRanges objects
isDisjoint-method GRangesList objects
isProperPair GappedAlignmentPairs objects
isProperPair-method GappedAlignmentPairs objects

-- K --

keepSeqlevels seqlevels utility functions
keepSeqlevels-method seqlevels utility functions

-- L --

last GappedAlignmentPairs objects
last-method GappedAlignmentPairs objects
left GappedAlignmentPairs objects
left-method GappedAlignmentPairs objects
length-method GRanges objects
length-method GappedAlignmentPairs objects
length-method GappedAlignments objects
length-method Seqinfo objects

-- M --

makeGRangesListFromFeatureFragments GRangesList objects
map-method Mapping ranges between sequences
match-method GRanges, GRangesList, GappedAlignments and GappedAlignmentPairs Interval Overlaps
merge-method Seqinfo objects

-- N --

names-method GRanges objects
names-method GappedAlignmentPairs objects
names-method GappedAlignments objects
names-method Seqinfo objects
names<--method GRanges objects
names<--method GappedAlignmentPairs objects
names<--method GappedAlignments objects
names<--method Seqinfo objects
narrow-method GappedAlignments objects
nearest-method GRanges objects
ngap-method GappedAlignments objects

-- O --

order-method Comparing and ordering genomic ranges

-- P --

pgap-method Set operations on GRanges/GRangesList/GappedAlignments objects
pintersect-method Set operations on GRanges/GRangesList/GappedAlignments objects
precede-method GRanges objects
psetdiff-method Set operations on GRanges/GRangesList/GappedAlignments objects
punion-method Set operations on GRanges/GRangesList/GappedAlignments objects

-- Q --

qnarrow GappedAlignments objects
qnarrow-method GappedAlignments objects
queryLoc2refLoc CIGAR utility functions
queryLocs2refLocs CIGAR utility functions
qwidth GappedAlignments objects
qwidth-method GappedAlignments objects

-- R --

range-method GRanges objects
range-method GRangesList objects
ranges-method GRanges objects
ranges-method GRangesList objects
ranges-method GappedAlignments objects
ranges<--method GRanges objects
ranges<--method GRangesList objects
rank-method Comparing and ordering genomic ranges
readGappedAlignmentPairs GappedAlignmentPairs objects
readGappedAlignments GappedAlignments objects
reduce-method GRanges objects
reduce-method GRangesList objects
renameSeqlevels seqlevels utility functions
renameSeqlevels-method seqlevels utility functions
resize-method GRanges objects
restrict-method GRanges objects
restrict-method GRangesList objects
rglist GappedAlignments objects
rglist-method GappedAlignments objects
right GappedAlignmentPairs objects
right-method GappedAlignmentPairs objects
rname GappedAlignments objects
rname-method GappedAlignments objects
rname<- GappedAlignments objects
rname<--method GappedAlignments objects
rowData SummarizedExperiment instances
rowData-method SummarizedExperiment instances
rowData<- SummarizedExperiment instances
rowData<--method SummarizedExperiment instances

-- S --

score-method GRanges objects
score-method GRangesList objects
selectEncodingWithCompatibleStrand encodeOverlaps methods and related utilities
Seqinfo Seqinfo objects
seqinfo Accessing sequence information
Seqinfo-class Seqinfo objects
seqinfo-method GRanges objects
seqinfo-method GRangesList objects
seqinfo-method GappedAlignmentPairs objects
seqinfo-method GappedAlignments objects
seqinfo-method Accessing sequence information
seqinfo<- Accessing sequence information
seqinfo<--method GRanges objects
seqinfo<--method GRangesList objects
seqinfo<--method GappedAlignmentPairs objects
seqinfo<--method GappedAlignments objects
seqinfo<--method Accessing sequence information
seqlengths Accessing sequence information
seqlengths-method Seqinfo objects
seqlengths-method Accessing sequence information
seqlengths<- Accessing sequence information
seqlengths<--method Seqinfo objects
seqlengths<--method Accessing sequence information
seqlevels Accessing sequence information
seqlevels-method Seqinfo objects
seqlevels-method Accessing sequence information
seqlevels<- Accessing sequence information
seqlevels<--method Seqinfo objects
seqlevels<--method Accessing sequence information
seqnames Accessing sequence information
seqnames-method GRanges objects
seqnames-method GRangesList objects
seqnames-method GappedAlignmentPairs objects
seqnames-method GappedAlignments objects
seqnames-method Seqinfo objects
seqnames-method Accessing sequence information
seqnames<- Accessing sequence information
seqnames<--method GRanges objects
seqnames<--method GRangesList objects
seqnames<--method GappedAlignments objects
seqnames<--method Seqinfo objects
seqselect-method GRanges objects
seqselect<--method GRanges objects
setdiff-method Set operations on GRanges/GRangesList/GappedAlignments objects
setops-methods Set operations on GRanges/GRangesList/GappedAlignments objects
shift-method GRanges objects
shift-method GRangesList objects
show-method GRanges objects
show-method GRangesList objects
show-method GappedAlignmentPairs objects
show-method GappedAlignments objects
show-method Seqinfo objects
show-method SummarizedExperiment instances
SimpleGenomicRangesList-class GenomicRangesList objects
sort-method Comparing and ordering genomic ranges
split-method GRanges objects
splitCigar CIGAR utility functions
start-method GRanges objects
start-method GRangesList objects
start-method GappedAlignments objects
start<--method GRanges objects
start<--method GRangesList objects
strand-method GRanges objects
strand-method GRangesList objects
strand-method GappedAlignmentPairs objects
strand-method GappedAlignments objects
strand-method Strand utilities
strand-utils Strand utilities
strand<--method GRanges objects
strand<--method GRangesList objects
strand<--method GappedAlignments objects
strand<--method Strand utilities
subsetByOverlaps-method GRanges, GRangesList, GappedAlignments and GappedAlignmentPairs Interval Overlaps
summarizeCigarTable CIGAR utility functions
SummarizedExperiment SummarizedExperiment instances
SummarizedExperiment-class SummarizedExperiment instances
SummarizedExperiment-method SummarizedExperiment instances
summarizeOverlaps Count reads that map to genomic features
summarizeOverlaps-method Count reads that map to genomic features

-- U --

Union Count reads that map to genomic features
union-method Set operations on GRanges/GRangesList/GappedAlignments objects
unique-method Comparing and ordering genomic ranges
unlist-method GappedAlignmentPairs objects
updateObject-method GRanges objects
updateObject-method GRangesList objects
updateObject-method GappedAlignments objects
updateObject-method Seqinfo objects

-- V --

validCigar CIGAR utility functions

-- W --

width-method GRanges objects
width-method GRangesList objects
width-method GappedAlignments objects
width<--method GRanges objects
width<--method GRangesList objects
window-method GRanges objects

-- misc --

$-method SummarizedExperiment instances
$<--method SummarizedExperiment instances
%in%-method GRanges, GRangesList, GappedAlignments and GappedAlignmentPairs Interval Overlaps
<-method Comparing and ordering genomic ranges
<=-method Comparing and ordering genomic ranges
==-method Comparing and ordering genomic ranges
>-method Comparing and ordering genomic ranges
>=-method Comparing and ordering genomic ranges
[-method GRanges objects
[-method GRangesList objects
[-method GappedAlignmentPairs objects
[-method GappedAlignments objects
[-method Seqinfo objects
[-method SummarizedExperiment instances
[<--method GRanges objects
[<--method GRangesList objects
[<--method SummarizedExperiment instances
[[-method GappedAlignmentPairs objects
[[-method SummarizedExperiment instances
[[<--method GRangesList objects
[[<--method SummarizedExperiment instances