Class "Genome\_intervals"
Description
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).
Slots
.Data
:See
Intervals_full
annotation
:A
"data.frame"
with the same number of rows as.Data
. It has a column namedseq_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 namedinter_base
that is logical and does not contain missing values.inter_base
isFALSE
if the interval is to be understood as an interval over bases (such as codingsequence) andTRUE
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 positionn
indicates the space between basen
andn+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")
: ... coerce
signature(from = "Genome_intervals", to = "data.frame")
: ... 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")
: ... seqnames
signature(x = "Genome_intervals")
: ... seqnames<
signature(x = "Genome_intervals")
: ... size
signature(x = "Genome_intervals")
: ... type<
signature(x = "Genome_intervals")
: ... which\_nearest

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. SeeIntervals_full
for further details.  width

Returns the interval length as the number of bp covered (base interval) or spanned(interbase interval). Similar to the
IRanges
packagewidth
function.
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
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)
