| Genome_intervals-class {genomeIntervals} | R Documentation |
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).
.Data:Intervals_full annotation:"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:Intervals_full type:Intervals_full
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.
signature(x = "Genome_intervals"): ... signature(x = "Genome_intervals"): ... signature(x = "Genome_intervals"): ... signature(x = "Genome_intervals"): ... signature(x = "Genome_intervals"): ... signature(object = "Genome_intervals"): ... signature(object = "Genome_intervals"): ... signature(from = "Genome_intervals", to = "Intervals_full"): ... signature(from = "Genome_intervals", to = "character"): ... signature(from = "Genome_intervals", to = "Genome_intervals"): ... signature(x = "Genome_intervals"): ... signature(x = "Genome_intervals"): ... signature(x = "Genome_intervals"): ... signature(x = "Genome_intervals"): ... signature(from = "Genome_intervals", to = "Genome_intervals"): ... signature(x = "Genome_intervals"): ... signature(x = "Genome_intervals"): ... signature(x = "Genome_intervals"): ... signature(x = "Genome_intervals"): ... signature(x = "Genome_intervals"): ...
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.
Genome_intervals_stranded for a derived class that allows stranded genomic intervals.
# 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)