Genome_intervals_stranded-class {genomeIntervals}R Documentation

Class "Genome_intervals_stranded"

Description

A set of genomic intervals with a specified strand.

Slots

.Data:
See Genome_intervals
annotation:
A data.frame (see Genome_intervals for basic requirements). The annotation moreover has a strand column that is a factor with exactly two levels(typically "+" and "-").
closed:
See Genome_intervals
type:
See Genome_intervals

Extends

Class "Genome_intervals", directly. Class "Intervals_full", by class "Genome_intervals", distance 2. Class "Intervals_virtual", by class "Genome_intervals", distance 3. Class "matrix", by class "Genome_intervals", distance 4. Class "array", by class "Genome_intervals", distance 5. Class "structure", by class "Genome_intervals", distance 6. Class "vector", by class "Genome_intervals", distance 7, with explicit coerce.

Methods

coerce
signature(from = "Genome_intervals_stranded", to = "character"): ...
distance_to_nearest
signature(from = "Genome_intervals_stranded", to = "Genome_intervals_stranded"): ...
interval_complement
signature(x = "Genome_intervals_stranded"): ...
interval_intersection
signature(x = "Genome_intervals_stranded"): ...
interval_overlap
signature(to = "Genome_intervals_stranded", from = "Genome_intervals_stranded"): ...
interval_union
signature(x = "Genome_intervals_stranded"): ...
strand
signature(x = "Genome_intervals_stranded"): ...
strand<-
signature(x = "Genome_intervals_stranded"): ...

See Also

Genome_intervals the parent class without strand.

Examples


# The "Genome_intervals_stranded" class
j <- new(
         "Genome_intervals_stranded",
         matrix(
                c(1,2,  
                  3,5,
                  4,6,
                  8,9
                  ),
                byrow = TRUE,
                ncol = 2
         ),
         closed = matrix(
                                c(
                                        FALSE, FALSE,
                                        TRUE, FALSE,
                                        TRUE, TRUE,
                                        TRUE, FALSE
                                 ),
                                byrow = TRUE,
                        ncol = 2
                        ),
     annotation = data.frame(
                                seq_name = factor( c("chr01","chr01", "chr02","chr02") ),
                                        strand = factor( c("+", "+", "+", "-") ),
                                        inter_base = c(FALSE,FALSE,FALSE,TRUE)
                                        )
         )

## print
print(j)

## size of each interval as count of included bases 
size(j)

## close intervals left and right (canonical representation)
close_intervals(j)

[Package genomeIntervals version 1.0.1 Index]