Representation and manipulation of genomic intervals

Documentation for package ‘GenomicRanges’ version 1.0.9

DESCRIPTION file.
Overview of user guides and package vignettes; browse directory.

Help Pages

-- --

%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