Operations on genomic intervals

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Documentation for package ‘genomeIntervals’ version 1.65.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

genomeIntervals-package	Operations on genomic intervals
$-method	Class "Genome\_intervals"
$<--method	Class "Genome\_intervals"
.readGff3	readGff3
annotation	Class "Genome\_intervals"
annotation-method	Class "Genome\_intervals"
annotation<-	Class "Genome\_intervals"
annotation<--method	Class "Genome\_intervals"
as	Coercion methods of the genomeIntervals package
as-method	Coercion methods of the genomeIntervals package
c	c extension for the 'genomeIntervals package'
c-method	c extension for the 'genomeIntervals package'
coerce-method	Class "Genome\_intervals"
coerce-method	Coercion methods of the genomeIntervals package
coerce-method	Class "Genome\_intervals\_stranded"
core_annotated	Genome intervals with minimal annotation
core_annotated-method	Genome intervals with minimal annotation
distance_to_nearest	Distance in bases to the closest interval(s)
distance_to_nearest-method	Distance in bases to the closest interval(s)
GenomeIntervals	Constructor function for genomeIntervals objects
genomeIntervals	Operations on genomic intervals
genomeIntervals coercion methods	Coercion methods of the genomeIntervals package
GenomeIntervals-constructor	Constructor function for genomeIntervals objects
Genome_intervals deprecated functions	The following function have been deprecated: • 'seq_name' • 'seq_name<-'
Genome_intervals-class	Class "Genome\_intervals"
Genome_intervals-ordering	Ordering methods for Genome intervals
Genome_intervals_stranded-class	Class "Genome\_intervals\_stranded"
gen_ints	Genome Intervals examples
getGffAttribute	Pull one or more key/value pairs from gffAttributes strings
i	Genome Intervals examples
interval_complement	Genome interval set operations
interval_complement-method	Genome interval set operations
interval_intersection	Genome interval set operations
interval_intersection-method	Genome interval set operations
interval_overlap	Assess overlap from one set of genomic intervals to another
interval_overlap-method	Assess overlap from one set of genomic intervals to another
interval_union	Genome interval set operations
interval_union-method	Genome interval set operations
inter_base	Class "Genome\_intervals"
inter_base-method	Class "Genome\_intervals"
inter_base<-	Class "Genome\_intervals"
inter_base<--method	Class "Genome\_intervals"
j	Genome Intervals examples
k	Genome Intervals examples
order	Ordering methods for Genome intervals
order-method	Ordering methods for Genome intervals
parseGffAttributes	Parse out the gffAttributes column of a Genome\_intervals object
rank	Ordering methods for Genome intervals
rank-method	Ordering methods for Genome intervals
readBasePairFeaturesGff3	readGff3
readBasePairFeaturesGff3-method	readGff3
readGff3	readGff3
readGff3-method	readGff3
readZeroLengthFeaturesGff3	readGff3
readZeroLengthFeaturesGff3-method	readGff3
seqnames-method	Class "Genome\_intervals"
seqnames<--method	Class "Genome\_intervals"
seq_name	The following function have been deprecated: • 'seq_name' • 'seq_name<-'
seq_name-method	The following function have been deprecated: • 'seq_name' • 'seq_name<-'
seq_name<-	The following function have been deprecated: • 'seq_name' • 'seq_name<-'
seq_name<--method	The following function have been deprecated: • 'seq_name' • 'seq_name<-'
show-method	Class "Genome\_intervals"
size-method	Class "Genome\_intervals"
sort	Ordering methods for Genome intervals
sort-method	Ordering methods for Genome intervals
strand	Class "Genome\_intervals\_stranded"
strand-method	Class "Genome\_intervals\_stranded"
strand<-	Class "Genome\_intervals\_stranded"
strand<--method	Class "Genome\_intervals"
strand<--method	Class "Genome\_intervals\_stranded"
type<--method	Class "Genome\_intervals"
which_nearest-method	Class "Genome\_intervals"
width-method	Class "Genome\_intervals"
writeGff3	readGff3
writeGff3-method	readGff3
xtfrm	Ordering methods for Genome intervals
xtfrm-method	Ordering methods for Genome intervals
[-method	Class "Genome\_intervals"
[<--method	Class "Genome\_intervals"
[[-method	Class "Genome\_intervals"
[[<--method	Class "Genome\_intervals"