Genome_intervals-class {genomeIntervals}R Documentation

Class "Genome_intervals"

Description

A set of genomic intervals without specified strand. Genomic intervals are intervals over the integers with two further annotations: seq_name (a chromosome or more generally a sequence of origin) and inter_base (logical) that states whether the interval is to be understood as an interval over bases (such as coding-sequence) or inter-bases (such as restriction sites or insertion positions).

Slots

.Data:
See Intervals_full
annotation:
A "data.frame" with the same number of rows as .Data. It has a column named seq_name that is a factor and does not contain missing values. seq_name is used to represent the chromosome or more generally the sequence of origin of the intervals. annotation has a column named inter_base that is logical and does not contain missing values. inter_base is FALSE if the interval is to be understood as an interval over bases (such as coding-sequence) and TRUE if it is over inter-bases (such as restriction site or an insertion position). Like base intervals, inter-base interval are encoded over the integers. An inter-base at position n indicates the space between base n and n+1.
closed:
See Intervals_full
type:
See Intervals_full

Extends

Class "Intervals_full", directly. Class "Intervals_virtual", by class "Intervals_full", distance 2. Class "matrix", by class "Intervals_full", distance 3. Class "array", by class "Intervals_full", distance 4. Class "structure", by class "Intervals_full", distance 5. Class "vector", by class "Intervals_full", distance 6, with explicit coerce.

Methods

[
signature(x = "Genome_intervals"): ...
[[
signature(x = "Genome_intervals"): ...
[[<-
signature(x = "Genome_intervals"): ...
$
signature(x = "Genome_intervals"): ...
$<-
signature(x = "Genome_intervals"): ...
annotation
signature(object = "Genome_intervals"): ...
annotation<-
signature(object = "Genome_intervals"): ...
coerce
signature(from = "Genome_intervals", to = "Intervals_full"): ...
coerce
signature(from = "Genome_intervals", to = "character"): ...
distance_to_nearest
signature(from = "Genome_intervals", to = "Genome_intervals"): ...
inter_base
signature(x = "Genome_intervals"): ...
inter_base<-
signature(x = "Genome_intervals"): ...
interval_complement
signature(x = "Genome_intervals"): ...
interval_intersection
signature(x = "Genome_intervals"): ...
interval_overlap
signature(from = "Genome_intervals", to = "Genome_intervals"): ...
interval_union
signature(x = "Genome_intervals"): ...
seq_name
signature(x = "Genome_intervals"): ...
seq_name<-
signature(x = "Genome_intervals"): ...
size
signature(x = "Genome_intervals"): ...
type<-
signature(x = "Genome_intervals"): ...

Note

A Genome_intervals is a "Intervals_full" of type Z (i.e. a set of intervals over the integers). The annotation slot can carry further columns that can serve as annotations.

See Also

Genome_intervals_stranded for a derived class that allows stranded genomic intervals.

Examples

# The "Genome_intervals" class

i <- new(
         "Genome_intervals",
         matrix(
                c(1,2,  
                  3,5,
                  4,6,
                  8,9
                  ),
                byrow = TRUE,
                ncol = 2
         ),
         closed = matrix(
                                c(
                                        TRUE, FALSE,
                                        TRUE, FALSE,
                                        TRUE, TRUE,
                                        TRUE, FALSE
                                 ),
                                byrow = TRUE,
                        ncol = 2
                        ),
         annotation = data.frame(
                                        seq_name = factor(c("chr01","chr01", "chr02","chr02")),
                                        inter_base = c(FALSE, FALSE, TRUE, TRUE)
                                        )
         )
         
colnames(i) <- c( "start", "end" )

# print 
print(i)

# size (number of bases per interval)
size(i)

[Package genomeIntervals version 1.0.1 Index]