Representation and manipulation of genomic intervals


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Documentation for package ‘GenomicRanges’ version 1.0.7

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

-- --

%in%-method GRanges and GRangesList Interval Overlaps
%in%-method GappedAlignments objects

-- A --

as.data.frame-method GRanges objects
as.data.frame-method GRangesList objects
as.data.frame-method GappedAlignments objects

-- C --

c-method GRanges 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:GRanges GRanges objects
class:GRangesList GRangesList objects
coerce-method GRanges objects
coerce-method GRangesList objects
countOverlaps-method GRanges and GRangesList Interval Overlaps
countOverlaps-method GappedAlignments objects
coverage-method GRanges objects
coverage-method GRangesList objects
coverage-method GappedAlignments objects

-- D --

disjoin-method GRanges objects

-- E --

elementMetadata-method GRanges objects
elementMetadata-method GRangesList 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

-- F --

findOverlaps-method GRanges and GRangesList Interval Overlaps
findOverlaps-method GappedAlignments objects
flank-method GRanges objects

-- G --

GappedAlignments GappedAlignments objects
GappedAlignments-class GappedAlignments objects
gaps-method GRanges objects
GRanges GRanges objects
GRanges-class GRanges objects
GRangesList GRangesList objects
GRangesList-class GRangesList objects
grg GappedAlignments objects
grg-method GappedAlignments objects
grglist GappedAlignments objects
grglist-method GappedAlignments objects

-- I --

intersect-method GRanges and GRangesList Set and Parallel Set Operations

-- L --

length-method GRanges objects
length-method GappedAlignments objects

-- M --

match-method GRanges and GRangesList Interval Overlaps
match-method GappedAlignments objects

-- N --

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

-- P --

pintersect-method GRanges and GRangesList Set and Parallel Set Operations
pintersect-method GappedAlignments objects
psetdiff-method GRanges and GRangesList Set and Parallel Set Operations
punion-method GRanges and GRangesList Set and Parallel Set Operations

-- 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
ranges-method GRanges objects
ranges-method GRangesList objects
ranges<--method GRanges objects
ranges<--method GRangesList objects
readGappedAlignments GappedAlignments objects
reduce-method GRanges objects
resize-method GRanges objects
rev-method GRanges objects
rglist GappedAlignments objects
rglist-method GappedAlignments objects
rname GappedAlignments objects
rname-method GappedAlignments objects
rname<- GappedAlignments objects
rname<--method GappedAlignments objects

-- S --

seqlengths Accessing the sequence names and lengths stored in an object
seqlengths-method GRanges objects
seqlengths-method GRangesList objects
seqlengths-method GappedAlignments objects
seqlengths<- Accessing the sequence names and lengths stored in an object
seqlengths<--method GRanges objects
seqlengths<--method GRangesList objects
seqlengths<--method GappedAlignments objects
seqnames Accessing the sequence names and lengths stored in an object
seqnames-method GRanges objects
seqnames-method GRangesList objects
seqnames-method GappedAlignments objects
seqnames<- Accessing the sequence names and lengths stored in an object
seqnames<--method GRanges objects
seqnames<--method GRangesList objects
seqnames<--method GappedAlignments objects
seqselect-method GRanges objects
seqselect<--method GRanges objects
setdiff-method GRanges and GRangesList Set and Parallel Set Operations
shift-method GRanges objects
shift-method GRangesList objects
show-method GRanges objects
show-method GRangesList objects
show-method GappedAlignments objects
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
subsetByOverlaps-method GRanges and GRangesList Interval Overlaps
subsetByOverlaps-method GappedAlignments objects
summarizeCigarTable CIGAR utility functions

-- U --

union-method GRanges and GRangesList Set and Parallel Set Operations
unlist-method GRangesList 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 GRanges objects
[-method GRangesList objects
[-method GappedAlignments objects
[<--method GRanges objects
[<--method GRangesList objects