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" |