A set of genomic intervals without specified strand.
Genomic intervals are intervals over the integers with two further annotations: seqnames
(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 codingsequence) or interbases (such as restriction sites or insertion positions).
.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 codingsequence) and TRUE
if it is over interbases (such as restriction site or an insertion position).
Like base intervals, interbase interval are encoded over the integers. An interbase at position n
indicates the space between base n
and n+1
.
closed
:See Intervals_full
type
:See 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 = "data.frame")
: ...
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")
: ...
For each interval in Set1, finds nearest (least distant)
interval in Set2. Intervals on different chromsomes are
never considered 'near' to each other.
The returned value is a data.frame
with the number
of rows equal to the number of intervals in Set1. Each row
specifies the distance to the nearest interval in Set2 (a
0 means that the interval overlaps one or more intervals in Set2),
and the indices of near and overlapping intervals in Set2.
See Intervals_full
for further details.
Returns the interval length as the number of bp covered (base interval) or
spanned(interbase interval). Similar to the IRanges
package
width
function.
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45  # 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)
## convert to a data.frame
as(i,"data.frame")
## simpler way to construct a Genome_intervals object:
G < GenomeIntervals(start=c(1,3,4,5,10,8), end=c(5,5,6,8,11,9),
chromosome=rep(c("chr2","chrX","chr1"), each=2),
leftOpen=rep(c(FALSE, FALSE, TRUE), 2))
show(G)

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