Representation and manipulation of genomic intervals


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Documentation for package ‘GenomicRanges’ version 1.6.7

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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
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: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 GappedAlignments objects
coerce-method Seqinfo objects
colData SummarizedExperiment instances
colData-method SummarizedExperiment instances
colData<- SummarizedExperiment instances
colData<--method SummarizedExperiment instances
countGenomicOverlaps Count Read Hits in Genomic Features
countGenomicOverlaps-method Count Read Hits in Genomic Features
countOverlaps-method GRanges, GRangesList and GappedAlignments Interval Overlaps
coverage-method GRanges, GRangesList and GappedAlignments coverage
coverage-methods GRanges, GRangesList and GappedAlignments coverage

-- D --

dim-method SummarizedExperiment instances
dimnames-method SummarizedExperiment instances
dimnames<--method SummarizedExperiment instances
disjoin-method GRanges objects
distance-method GRanges objects
duplicated-method Ordering and comparing genomic ranges

-- E --

elementMetadata-method GRanges objects
elementMetadata-method GRangesList objects
elementMetadata-method GappedAlignments objects
elementMetadata<--method GRanges objects
elementMetadata<--method GRangesList objects
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

-- F --

findOverlaps-method GRanges, GRangesList and GappedAlignments Interval Overlaps
findOverlaps-methods GRanges, GRangesList and GappedAlignments Interval Overlaps
flank-method GRanges objects
flank-method GRangesList objects
follow-method GRanges objects

-- G --

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 Ordering and comparing 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
GRangesList GRangesList objects
GRangesList-class GRangesList objects
grg GappedAlignments objects
grglist GappedAlignments 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
isCircularWithKnownLength Accessing sequence information
isCircularWithKnownLength-method Seqinfo objects
isCircularWithKnownLength-method Accessing sequence information
isDisjoint-method GRanges objects
isDisjoint-method GRangesList objects

-- K --

keepSeqlevels seqlevels utility functions
keepSeqlevels-method seqlevels utility functions

-- L --

length-method GRanges objects
length-method GappedAlignments objects
length-method Seqinfo objects

-- M --

makeGRangesListFromFeatureFragments GRangesList objects
match-method GRanges, GRangesList and GappedAlignments Interval Overlaps
merge-method Seqinfo objects

-- N --

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

-- O --

order-method Ordering and comparing 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 Ordering and comparing genomic ranges
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
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 --

Seqinfo Seqinfo objects
seqinfo Accessing sequence information
Seqinfo-class Seqinfo objects
seqinfo-method GRanges objects
seqinfo-method GRangesList objects
seqinfo-method GappedAlignments objects
seqinfo<- Accessing sequence information
seqinfo<--method GRanges objects
seqinfo<--method GRangesList objects
seqinfo<--method GappedAlignments objects
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 GappedAlignments objects
seqnames-method Seqinfo objects
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 GappedAlignments objects
show-method Seqinfo objects
show-method SummarizedExperiment instances
SimpleGenomicRangesList-class GenomicRangesList objects
sort-method Ordering and comparing 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 Accessing strand information
strand-method GRanges objects
strand-method GRangesList objects
strand-method GappedAlignments objects
strand-method Accessing strand information
strand-methods Accessing strand information
strand<- Accessing strand information
strand<--method GRanges objects
strand<--method GRangesList objects
strand<--method GappedAlignments objects
subsetByOverlaps-method GRanges, GRangesList and GappedAlignments 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 Ordering and comparing genomic ranges
unlist-method GRangesList 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 --

%in%-method GRanges, GRangesList and GappedAlignments Interval Overlaps
<-method Ordering and comparing genomic ranges
<=-method Ordering and comparing genomic ranges
==-method Ordering and comparing genomic ranges
>-method Ordering and comparing genomic ranges
>=-method Ordering and comparing genomic ranges
[-method GRanges objects
[-method GRangesList objects
[-method GappedAlignments objects
[-method Seqinfo objects
[-method SummarizedExperiment instances
[<--method GRanges objects
[<--method GRangesList objects
[<--method SummarizedExperiment instances
[[<--method GRangesList objects