Genome_intervals_stranded-class {genomeIntervals} | R Documentation |
A set of genomic intervals with a specified strand.
.Data
:See Genome_intervals
annotation
:A 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
:See Genome_intervals
type
:See 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) ## simpler way to construct a Genome_intervals_stranded object GS <- GenomeIntervals(start=c(1,3,4,5,8,10), end=c(5,5,6,8,9,11), chromosome=rep(c("chr2","chrX","chr1"), each=2), strand=c("-","-","+","+","+","+") ) show(GS)