Operations on genomic intervals


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Documentation for package ‘genomeIntervals’ version 1.2.0

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genomeIntervals-package Operations on genomic intervals
$,Genome_intervals-method Class "Genome\_intervals"
$<-,Genome_intervals-method Class "Genome\_intervals"
annotation,Genome_intervals-method Class "Genome\_intervals"
annotation<-,Genome_intervals,ANY-method Class "Genome\_intervals"
c Combine genome intervals objects
c.Genome_intervals Combine genome intervals objects
c.Genome_intervals_stranded Combine genome intervals objects
coerce,Genome_intervals,character-method Class "Genome\_intervals"
coerce,Genome_intervals,Intervals_full-method Class "Genome\_intervals"
coerce,Genome_intervals_stranded,character-method Class "Genome\_intervals\_stranded"
core_annotated Genome intervals with minimal annotation
core_annotated,Genome_intervals-method Genome intervals with minimal annotation
core_annotated,Genome_intervals_stranded-method Genome intervals with minimal annotation
distance_to_nearest Distance in bases to the closest interval(s)
distance_to_nearest,Genome_intervals,Genome_intervals-method Distance in bases to the closest interval(s)
distance_to_nearest,Genome_intervals_stranded,Genome_intervals_stranded-method Distance in bases to the closest interval(s)
genomeIntervals Operations on genomic intervals
Genome_intervals-class Class "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,Genome_intervals-method Genome interval set operations
interval_complement,Genome_intervals_stranded-method Genome interval set operations
interval_intersection Genome interval set operations
interval_intersection,Genome_intervals-method Genome interval set operations
interval_intersection,Genome_intervals_stranded-method Genome interval set operations
interval_overlap Assess overlap from one set of genomic intervals to another
interval_overlap,ANY,missing-method Assess overlap from one set of genomic intervals to another
interval_overlap,Genome_intervals,Genome_intervals-method Assess overlap from one set of genomic intervals to another
interval_overlap,Genome_intervals_stranded,Genome_intervals_stranded-method Assess overlap from one set of genomic intervals to another
interval_overlap,missing,ANY-method Assess overlap from one set of genomic intervals to another
interval_union Genome interval set operations
interval_union,Genome_intervals-method Genome interval set operations
interval_union,Genome_intervals_stranded-method Genome interval set operations
inter_base Class "Genome\_intervals"
inter_base,Genome_intervals-method Class "Genome\_intervals"
inter_base<- Class "Genome\_intervals"
inter_base<-,Genome_intervals-method Class "Genome\_intervals"
j Genome Intervals examples
k Genome Intervals examples
parseGffAttributes Parse out the gffAttributes column of a Genome\_intervals object
readGff3 Make a Genome\_intervals\_stranded object from a GFF file
seq_name Class "Genome\_intervals"
seq_name,Genome_intervals-method Class "Genome\_intervals"
seq_name<- Class "Genome\_intervals"
seq_name<-,Genome_intervals-method Class "Genome\_intervals"
show,Genome_intervals-method Class "Genome\_intervals"
size,Genome_intervals-method Class "Genome\_intervals"
strand Class "Genome\_intervals\_stranded"
strand,Genome_intervals_stranded-method Class "Genome\_intervals\_stranded"
strand<- Class "Genome\_intervals\_stranded"
strand<-,Genome_intervals_stranded-method Class "Genome\_intervals\_stranded"
type<-,Genome_intervals-method Class "Genome\_intervals"
[,Genome_intervals-method Class "Genome\_intervals"
[<-,Genome_intervals,ANY,missing,Genome_intervals-method Class "Genome\_intervals"
[[,Genome_intervals-method Class "Genome\_intervals"
[[<-,Genome_intervals-method Class "Genome\_intervals"