Operations on genomic intervals

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Documentation for package ‘genomeIntervals’ version 1.12.0

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genomeIntervals-package Operations on genomic intervals
$-method Class "Genome\_intervals"
$<--method Class "Genome\_intervals"
annotation-method Class "Genome\_intervals"
annotation<--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-method Class "Genome\_intervals"
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-constructor Constructor function for genomeIntervals objects
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-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
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-method Class "Genome\_intervals"
seq_name<- Class "Genome\_intervals"
seq_name<--method Class "Genome\_intervals"
show-method Class "Genome\_intervals"
size-method Class "Genome\_intervals"
strand Class "Genome\_intervals\_stranded"
strand-method Class "Genome\_intervals\_stranded"
strand<- Class "Genome\_intervals\_stranded"
strand<--method Class "Genome\_intervals\_stranded"
type<--method Class "Genome\_intervals"
[-method Class "Genome\_intervals"
[<--method Class "Genome\_intervals"
[[-method Class "Genome\_intervals"
[[<--method Class "Genome\_intervals"