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: 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 coding-sequence) or inter-bases (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 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
: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")
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signature(x = "Genome_intervals")
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signature(x = "Genome_intervals")
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signature(x = "Genome_intervals")
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signature(x = "Genome_intervals")
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signature(object = "Genome_intervals")
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signature(object = "Genome_intervals")
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signature(from = "Genome_intervals", to = "Intervals_full")
: ...
signature(from = "Genome_intervals", to = "character")
: ...
signature(from = "Genome_intervals", to = "data.frame")
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signature(from = "Genome_intervals", to = "Genome_intervals")
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signature(x = "Genome_intervals")
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signature(x = "Genome_intervals")
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signature(x = "Genome_intervals")
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signature(x = "Genome_intervals")
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signature(from = "Genome_intervals", to = "Genome_intervals")
: ...
signature(x = "Genome_intervals")
: ...
signature(x = "Genome_intervals")
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signature(x = "Genome_intervals")
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signature(x = "Genome_intervals")
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signature(x = "Genome_intervals")
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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(inter-base 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.
# 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)