Representation and manipulation of genomic intervals


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Documentation for package ‘GenomicRanges’ version 1.12.1

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

-- A --

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

-- C --

c-method GAlignmentsList objects
c-method GRanges objects
c-method GappedAlignments objects
cbind-method SummarizedExperiment instances
checkConstraint Enforcing constraints thru Constraint objects
cigar GappedAlignments objects
cigar-method GAlignmentsList 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:GAlignmentsList GAlignmentsList 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 GAlignmentsList 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
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
countCompatibleOverlaps encodeOverlaps method for GRangesList objects, and related utilities
countMatches-method Comparing and ordering genomic ranges
countMatches-method Finding overlapping genomic ranges
countOverlaps-method SummarizedExperiment instances
countOverlaps-method Finding overlapping genomic ranges
coverage-method SummarizedExperiment instances
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 GRangesList objects
disjoin-method Inter range transformations of a GenomicRanges object
disjointBins-method SummarizedExperiment instances
disjointBins-method Inter range transformations of a GenomicRanges 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
duplicated-method Comparing and ordering genomic ranges
duplicated-method SummarizedExperiment instances
duplicated.GenomicRanges Comparing and ordering genomic ranges

-- E --

elementMetadata-method GAlignmentsList objects
elementMetadata-method GRangesList objects
elementMetadata-method SummarizedExperiment instances
elementMetadata<--method GAlignmentsList objects
elementMetadata<--method GRanges objects
elementMetadata<--method GRangesList objects
elementMetadata<--method GappedAlignmentPairs objects
elementMetadata<--method GappedAlignments objects
elementMetadata<--method SummarizedExperiment instances
encodeOverlaps-method encodeOverlaps method for GRangesList objects, and related utilities
encodeOverlaps-methods encodeOverlaps method for GRangesList objects, and related utilities
end-method GAlignmentsList objects
end-method GRanges objects
end-method GRangesList objects
end-method GappedAlignments 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
extractQueryStartInTranscript encodeOverlaps method for GRangesList objects, and related utilities
extractSkippedExonRanks encodeOverlaps method for GRangesList objects, and related utilities
extractSkippedExonRanks-method encodeOverlaps method for GRangesList objects, and related utilities
extractSpannedExonRanks encodeOverlaps method for GRangesList objects, and related utilities
extractSpannedExonRanks-method encodeOverlaps method for GRangesList objects, and related utilities
extractSteppedExonRanks encodeOverlaps method for GRangesList objects, and related utilities
extractSteppedExonRanks-method encodeOverlaps method for GRangesList objects, and related utilities

-- F --

findCompatibleOverlaps encodeOverlaps method for GRangesList objects, and related utilities
findCompatibleOverlaps-method encodeOverlaps method for GRangesList objects, and related utilities
findMatches-method Comparing and ordering genomic ranges
findMatches-method Finding overlapping genomic ranges
findOverlaps-method SummarizedExperiment instances
findOverlaps-method Finding overlapping genomic ranges
findOverlaps-methods Finding overlapping genomic ranges
findSpliceOverlaps Classify ranges (reads) as compatible with existing genomic annotations or as having novel splice events
findSpliceOverlaps-method Classify ranges (reads) as compatible with existing genomic annotations or as having novel splice events
findSpliceOverlaps-methods Classify ranges (reads) as compatible with existing genomic annotations or as having novel splice events
first GappedAlignmentPairs objects
first-method GappedAlignmentPairs objects
flank-method GRangesList objects
flank-method SummarizedExperiment instances
flank-method Intra range transformations of a GenomicRanges object
flipQuery encodeOverlaps method for GRangesList objects, and related utilities
follow-method SummarizedExperiment instances
follow-method Finding the nearest genomic range neighbor

-- G --

GAlignmentsList GAlignmentsList objects
GAlignmentsList-class GAlignmentsList objects
GappedAlignmentPairs GappedAlignmentPairs objects
GappedAlignmentPairs-class GappedAlignmentPairs objects
GappedAlignments GappedAlignments objects
GappedAlignments-class GappedAlignments objects
gaps-method Inter range transformations of a GenomicRanges object
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 GAlignmentsList objects
granges-method GappedAlignmentPairs objects
granges-method GappedAlignments objects
granges-method SummarizedExperiment instances
granges-method Mapping ranges between sequences
GRangesList GRangesList objects
GRangesList-class GRangesList objects
grglist GappedAlignments objects
grglist-method GAlignmentsList objects
grglist-method GappedAlignmentPairs objects
grglist-method GappedAlignments objects

-- I --

inter-range-methods Inter range transformations of a GenomicRanges object
intersect-method Seqinfo objects
intersect-method Set operations on GRanges/GRangesList/GappedAlignments objects
IntersectionNotEmpty Perform overlap queries between reads and genomic features
IntersectionStrict Perform overlap queries between reads and genomic features
intra-range-methods Intra range transformations of a GenomicRanges object
introns GappedAlignments objects
introns-method GAlignmentsList objects
introns-method GappedAlignmentPairs objects
introns-method GappedAlignments objects
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 method for GRangesList objects, and related utilities
isCompatibleWithSkippedExons-method encodeOverlaps method for GRangesList objects, and related utilities
isCompatibleWithSplicing encodeOverlaps method for GRangesList objects, and related utilities
isCompatibleWithSplicing-method encodeOverlaps method for GRangesList objects, and related utilities
isDisjoint-method GRangesList objects
isDisjoint-method SummarizedExperiment instances
isDisjoint-method Inter range transformations of a GenomicRanges object
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 --

makeGAlignmentsListFromFeatureFragments GAlignmentsList objects
makeGRangesListFromFeatureFragments GRangesList objects
makeSeqnameIds Assigns a unique ID to each unique sequence name
map-method Mapping ranges between sequences
match-method Comparing and ordering genomic ranges
match-method SummarizedExperiment instances
match-method Finding overlapping genomic ranges
mcols-method SummarizedExperiment instances
mcols<--method SummarizedExperiment instances
merge-method Seqinfo objects

-- N --

names-method GAlignmentsList objects
names-method GRanges objects
names-method GappedAlignmentPairs objects
names-method GappedAlignments objects
names-method Seqinfo objects
names<--method GAlignmentsList objects
names<--method GRanges objects
names<--method GappedAlignmentPairs objects
names<--method GappedAlignments objects
names<--method Seqinfo objects
narrow-method SummarizedExperiment instances
narrow-method Intra range transformations of a GenomicRanges object
nearest-method SummarizedExperiment instances
nearest-method Finding the nearest genomic range neighbor
nearest-methods Finding the nearest genomic range neighbor
ngap-method GAlignmentsList objects
ngap-method GappedAlignmentPairs objects
ngap-method GappedAlignments objects

-- O --

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

-- P --

pgap-method Set operations on GRanges/GRangesList/GappedAlignments objects
phicoef Calculate the "phi coefficient" between two binary variables
pintersect-method Set operations on GRanges/GRangesList/GappedAlignments objects
precede-method SummarizedExperiment instances
precede-method Finding the nearest genomic range neighbor
promoters-method GRangesList objects
promoters-method Intra range transformations of a GenomicRanges object
psetdiff-method Set operations on GRanges/GRangesList/GappedAlignments objects
punion-method Set operations on GRanges/GRangesList/GappedAlignments objects

-- Q --

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

-- R --

range-method GRangesList objects
range-method Inter range transformations of a GenomicRanges object
ranges-method GAlignmentsList objects
ranges-method GRanges objects
ranges-method GRangesList objects
ranges-method GappedAlignments 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
readGAlignmentsList GAlignmentsList objects
readGappedAlignmentPairs GappedAlignmentPairs objects
readGappedAlignments GappedAlignments objects
reduce-method GRangesList objects
reduce-method Inter range transformations of a GenomicRanges object
renameSeqlevels seqlevels utility functions
renameSeqlevels-method seqlevels utility functions
resize-method SummarizedExperiment instances
resize-method Intra range transformations of a GenomicRanges object
restrict-method GRangesList objects
restrict-method SummarizedExperiment instances
restrict-method Intra range transformations of a GenomicRanges object
rglist GappedAlignments objects
rglist-method GAlignmentsList objects
rglist-method GappedAlignments objects
right GappedAlignmentPairs objects
right-method GappedAlignmentPairs objects
rname GappedAlignments objects
rname-method GAlignmentsList objects
rname-method GappedAlignments objects
rname<- GappedAlignments objects
rname<--method GAlignmentsList 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 method for GRangesList objects, and related utilities
Seqinfo Seqinfo objects
seqinfo Accessing sequence information
Seqinfo-class Seqinfo objects
seqinfo-method GAlignmentsList objects
seqinfo-method GRanges objects
seqinfo-method GRangesList objects
seqinfo-method GappedAlignmentPairs objects
seqinfo-method GappedAlignments objects
seqinfo-method SummarizedExperiment instances
seqinfo-method Accessing sequence information
seqinfo<- Accessing sequence information
seqinfo<--method GAlignmentsList objects
seqinfo<--method GRanges objects
seqinfo<--method GRangesList objects
seqinfo<--method GappedAlignmentPairs objects
seqinfo<--method GappedAlignments objects
seqinfo<--method SummarizedExperiment instances
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 GAlignmentsList objects
seqnames-method GRanges objects
seqnames-method GRangesList objects
seqnames-method GappedAlignmentPairs objects
seqnames-method GappedAlignments objects
seqnames-method Seqinfo objects
seqnames-method SummarizedExperiment instances
seqnames-method Accessing sequence information
seqnames<- Accessing sequence information
seqnames<--method GAlignmentsList objects
seqnames<--method GRanges objects
seqnames<--method GRangesList objects
seqnames<--method GappedAlignments objects
seqnames<--method Seqinfo objects
seqnameStyle Accessing sequence information
seqnameStyle-method Seqinfo objects
seqnameStyle-method Accessing sequence information
seqnameStyle<- Accessing sequence information
seqnameStyle<--method Seqinfo objects
seqnameStyle<--method Accessing sequence information
seqselect-method GRanges objects
seqselect-method SummarizedExperiment instances
seqselect<--method GRanges objects
seqselect<--method SummarizedExperiment instances
setdiff-method Set operations on GRanges/GRangesList/GappedAlignments objects
setops-methods Set operations on GRanges/GRangesList/GappedAlignments objects
shift-method GRangesList objects
shift-method SummarizedExperiment instances
shift-method Intra range transformations of a GenomicRanges object
show-method GAlignmentsList 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 SummarizedExperiment instances
split-method SummarizedExperiment instances
splitAsListReturnedClass,GRange GRanges objects
splitAsListReturnedClass-method GRanges objects
splitAsListReturnedClass-method GappedAlignments objects
splitAsListReturnedClass-method SummarizedExperiment instances
splitCigar CIGAR utility functions
start-method GAlignmentsList objects
start-method GRanges objects
start-method GRangesList objects
start-method GappedAlignments objects
start-method SummarizedExperiment instances
start<--method GRanges objects
start<--method GRangesList objects
start<--method SummarizedExperiment instances
strand-method GAlignmentsList objects
strand-method GRanges objects
strand-method GRangesList objects
strand-method GappedAlignmentPairs objects
strand-method GappedAlignments objects
strand-method SummarizedExperiment instances
strand-method Strand utilities
strand-utils Strand utilities
strand<--method GAlignmentsList objects
strand<--method GRanges objects
strand<--method GRangesList objects
strand<--method GappedAlignmentPairs objects
strand<--method GappedAlignments objects
strand<--method SummarizedExperiment instances
strand<--method Strand utilities
subsetByOverlaps-method SummarizedExperiment instances
subsetByOverlaps-method Finding overlapping genomic ranges
summarizeCigarTable CIGAR utility functions
SummarizedExperiment SummarizedExperiment instances
SummarizedExperiment-class SummarizedExperiment instances
SummarizedExperiment-method SummarizedExperiment instances
summarizeOverlaps Perform overlap queries between reads and genomic features
summarizeOverlaps-method Perform overlap queries between reads and genomic features

-- T --

trim-method Intra range transformations of a GenomicRanges object

-- U --

Union Perform overlap queries between reads and genomic features
union-method Set operations on GRanges/GRangesList/GappedAlignments objects
unlist-method GappedAlignmentPairs objects
updateObject-method GAlignmentsList objects
updateObject-method GRanges objects
updateObject-method GRangesList objects
updateObject-method GappedAlignments objects
updateObject-method Seqinfo objects
updateObject-method SummarizedExperiment instances

-- V --

validCigar CIGAR utility functions
values-method SummarizedExperiment instances
values<--method SummarizedExperiment instances

-- W --

width-method GAlignmentsList objects
width-method GRanges objects
width-method GRangesList objects
width-method GappedAlignments 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
%in%-method Comparing and ordering genomic ranges
%in%-method SummarizedExperiment instances
%in%-method Finding overlapping genomic ranges
<=-method Comparing and ordering genomic ranges
==-method Comparing and ordering genomic ranges
[-method GAlignmentsList objects
[-method GRanges objects
[-method GRangesList objects
[-method GappedAlignmentPairs objects
[-method GappedAlignments objects
[-method Seqinfo objects
[-method SummarizedExperiment instances
[<--method GAlignmentsList objects
[<--method GRanges objects
[<--method GRangesList objects
[<--method SummarizedExperiment instances
[[-method GappedAlignmentPairs objects
[[-method SummarizedExperiment instances
[[<--method GAlignmentsList objects
[[<--method GRangesList objects
[[<--method SummarizedExperiment instances