| Genome_intervals_stranded-class {genomeIntervals} | R Documentation |
A set of genomic intervals with a specified strand.
.Data:Genome_intervals annotation: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:Genome_intervals type:Genome_intervals
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.
signature(from = "Genome_intervals_stranded", to = "character"): ... signature(from = "Genome_intervals_stranded", to = "Genome_intervals_stranded"): ... signature(x = "Genome_intervals_stranded"): ... signature(x = "Genome_intervals_stranded"): ... signature(to = "Genome_intervals_stranded", from = "Genome_intervals_stranded"): ... signature(x = "Genome_intervals_stranded"): ... signature(x = "Genome_intervals_stranded"): ... signature(x = "Genome_intervals_stranded"): ...
Genome_intervals the parent class without strand.
# 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)