Description Usage Arguments Details See Also Examples
An order is defined on genome intervals and stranded genome intervals to allow sort(), order() and rank().
1 2 3 4 5 6 7 8 9 10 11 12  ## S4 method for signature 'Genome_intervals'
order(..., na.last=TRUE, decreasing=FALSE)
## S4 method for signature 'Genome_intervals_stranded'
order(..., na.last=TRUE, decreasing=FALSE)
## S4 method for signature 'Genome_intervals'
sort(x, decreasing=FALSE, ...)
## S4 method for signature 'Genome_intervals'
rank(x, na.last=TRUE, ties.method=c("average", "first", "last", "random", "max", "min"), ...)
## S4 method for signature 'Genome_intervals'
xtfrm(x)

x 
Objects of class 
... 
Objects of class 
na.last 
Ignored for ordering 
decreasing 

ties.method 
A character string specifying how ties are treated. Only 
An order on Genome_intervals entries is defined by sorting by 1. seqnames 2. start, where closed start & not interbase < closed start & interbase < open start & not interbase < open start & interbase 3. stop, where open stop & not interbase < open stop & interbase < closed stop & not interbase < closed stop & interbase 4. strand (for Genome_intervals_stranded object)
The factors seqnames
and strand
are sorted according to their levels (default R behavior).
The primitive is implemented in xtfrm
which is then called by the other methods.
Hence, the order
, sort
and rank
methods are consistent.
order(..., na.last=TRUE, decreasing=TRUE)
:
return a permutation which rearranges its first argument
into ascending or descending order, breaking ties by further
arguments.
See order
in the base package for more details.
na.last
is ignored for Genome_intervals
objects.
rank(x, na.last=TRUE, ties.method=c("average", "first", "last", "random", "max", "min"), ...)
:
Return the sample ranks of the (stranded) genome intervals in x
.
See rank
in the base package for more details.
sort(x)
:
Sort x
.
See sort
in the base package for more details.
xtfrm(x)
:
Auxiliary function that produces a numeric vector which will sort in the same order as 'x' x
.
See xtfrm
in the base package for more details.
Workhorse for the other methods
Genome_intervals
Genome_intervals_stranded
order
,
sort
,
rank
,
xtfrm
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24  ## an example with ties
gi = GenomeIntervals(c("chr2", "chr2", "chr1", "chr1"), c(1,1,10,10), c(5,3,12,12) )
sort(gi)
rank(gi)
order(gi)
## Define order on seqnames at your convenience
## by specifying the order of the levels
## compare:
gi = GenomeIntervals(
c("chr2", "chr2", "chr10", "chr10"),
c(1,1,10,10),
c(5,3,12,12)
)
sort(gi)
## with:
gi2 = GenomeIntervals(
factor(c("chr2", "chr2", "chr10", "chr10"), levels=c("chr2", "chr10")),
c(1,1,10,10),
c(5,3,12,12)
)
sort(gi2)

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