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" |