findOverlaps-methods: Finding overlapping genomic ranges
In GenomicRanges: Representation and manipulation of genomic intervals
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
Various methods for finding/counting overlaps between objects containing
genomic ranges. This man page describes the methods that operate on
GenomicRanges and GRangesList objects.
NOTE: The findOverlaps generic function
and methods for IntegerRanges and
IntegerRangesList objects are defined and
documented in the IRanges package.
The methods for GAlignments,
GAlignmentPairs, and
GAlignmentsList objects are defined and
documented in the GenomicAlignments package.
GenomicRanges and GRangesList objects also support
countOverlaps, overlapsAny, and subsetByOverlaps
thanks to the default methods defined in the IRanges package and
to the findOverlaps and countOverlaps methods defined in
this package and documented below.
Usage
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## S4 method for signature 'GenomicRanges,GenomicRanges'
findOverlaps(query, subject,
maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
select=c("all", "first", "last", "arbitrary"),
ignore.strand=FALSE)
## S4 method for signature 'GenomicRanges,GenomicRanges'
countOverlaps(query, subject,
maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
ignore.strand=FALSE)
Arguments
query, subject
A GRanges or GRangesList object.
maxgap, minoverlap, type
See ?findOverlaps in the IRanges package
for a description of these arguments.
select
When select is "all" (the default), the results are
returned as a Hits object.
Otherwise the returned value is an integer vector parallel to query
(i.e. same length) containing the first, last, or arbitrary overlapping
interval in subject, with NA indicating intervals that did
not overlap any intervals in subject.
ignore.strand
When set to TRUE, the strand information is ignored in the
overlap calculations.
Details
When the query and the subject are GRanges or
GRangesList objects, findOverlaps uses the triplet
(sequence name, range, strand) to determine which features (see
paragraph below for the definition of feature) from the query
overlap which features in the subject, where a strand value
of "*" is treated as occurring on both the "+" and
"-" strand.
An overlap is recorded when a feature in the query and a feature
in the subject have the same sequence name, have a compatible
pairing of strands (e.g. "+"/"+", "-"/"-",
"*"/"+", "*"/"-", etc.), and satisfy the
interval overlap requirements.
In the context of findOverlaps, a feature is a collection of
ranges that are treated as a single entity. For GRanges objects,
a feature is a single range; while for GRangesList objects,
a feature is a list element containing a set of ranges. In the results,
the features are referred to by number, which run from 1 to
length(query)/length(subject).
For type="equal" with GRangesList objects, query[[i]]
matches subject[[j]] iff for each range in query[[i]]
there is an identical range in subject[[j]], and vice versa.
Value
For findOverlaps either a Hits object when
select="all" or an integer vector otherwise.
For countOverlaps an integer vector containing the tabulated
query overlap hits.
Author(s)
P. Aboyoun, S. Falcon, M. Lawrence, and H. Pag<c3><a8>s
See Also
The Hits class for representing a set of hits between 2
vector-like objects.
The findOverlaps generic function defined
in the IRanges package.
The GNCList constructor and class for preprocessing and
representing a GenomicRanges or object as a data structure
based on Nested Containment Lists.
The GRanges and GRangesList classes.
Examples
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## ---------------------------------------------------------------------
## BASIC EXAMPLES
## ---------------------------------------------------------------------
## GRanges object:
gr <- GRanges(
seqnames=Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
ranges=IRanges(1:10, width=10:1, names=head(letters,10)),
strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
score=1:10,
GC=seq(1, 0, length=10)
)
gr
## GRangesList object:
gr1 <- GRanges(seqnames="chr2", ranges=IRanges(4:3, 6),
strand="+", score=5:4, GC=0.45)
gr2 <- GRanges(seqnames=c("chr1", "chr1"),
ranges=IRanges(c(7,13), width=3),
strand=c("+", "-"), score=3:4, GC=c(0.3, 0.5))
gr3 <- GRanges(seqnames=c("chr1", "chr2"),
ranges=IRanges(c(1, 4), c(3, 9)),
strand=c("-", "-"), score=c(6L, 2L), GC=c(0.4, 0.1))
grl <- GRangesList("gr1"=gr1, "gr2"=gr2, "gr3"=gr3)
## Overlapping two GRanges objects:
table(!is.na(findOverlaps(gr, gr1, select="arbitrary")))
countOverlaps(gr, gr1)
findOverlaps(gr, gr1)
subsetByOverlaps(gr, gr1)
countOverlaps(gr, gr1, type="start")
findOverlaps(gr, gr1, type="start")
subsetByOverlaps(gr, gr1, type="start")
findOverlaps(gr, gr1, select="first")
findOverlaps(gr, gr1, select="last")
findOverlaps(gr1, gr)
findOverlaps(gr1, gr, type="start")
findOverlaps(gr1, gr, type="within")
findOverlaps(gr1, gr, type="equal")
## ---------------------------------------------------------------------
## MORE EXAMPLES
## ---------------------------------------------------------------------
table(!is.na(findOverlaps(gr, gr1, select="arbitrary")))
countOverlaps(gr, gr1)
findOverlaps(gr, gr1)
subsetByOverlaps(gr, gr1)
## Overlaps between a GRanges and a GRangesList object:
table(!is.na(findOverlaps(grl, gr, select="first")))
countOverlaps(grl, gr)
findOverlaps(grl, gr)
subsetByOverlaps(grl, gr)
countOverlaps(grl, gr, type="start")
findOverlaps(grl, gr, type="start")
subsetByOverlaps(grl, gr, type="start")
findOverlaps(grl, gr, select="first")
table(!is.na(findOverlaps(grl, gr1, select="first")))
countOverlaps(grl, gr1)
findOverlaps(grl, gr1)
subsetByOverlaps(grl, gr1)
countOverlaps(grl, gr1, type="start")
findOverlaps(grl, gr1, type="start")
subsetByOverlaps(grl, gr1, type="start")
findOverlaps(grl, gr1, select="first")
## Overlaps between two GRangesList objects:
countOverlaps(grl, rev(grl))
findOverlaps(grl, rev(grl))
subsetByOverlaps(grl, rev(grl))
Example output
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
GRanges object with 10 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
a chr1 1-10 - | 1 1
b chr2 2-10 + | 2 0.888888888888889
c chr2 3-10 + | 3 0.777777777777778
d chr2 4-10 * | 4 0.666666666666667
e chr1 5-10 * | 5 0.555555555555556
f chr1 6-10 + | 6 0.444444444444444
g chr3 7-10 + | 7 0.333333333333333
h chr3 8-10 + | 8 0.222222222222222
i chr3 9-10 - | 9 0.111111111111111
j chr3 10 - | 10 0
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
FALSE TRUE
7 3
a b c d e f g h i j
0 2 2 2 0 0 0 0 0 0
Hits object with 6 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 2 2
[2] 2 1
[3] 3 2
[4] 3 1
[5] 4 2
[6] 4 1
-------
queryLength: 10 / subjectLength: 2
GRanges object with 3 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
b chr2 2-10 + | 2 0.888888888888889
c chr2 3-10 + | 3 0.777777777777778
d chr2 4-10 * | 4 0.666666666666667
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
a b c d e f g h i j
0 0 1 1 0 0 0 0 0 0
Hits object with 2 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 3 2
[2] 4 1
-------
queryLength: 10 / subjectLength: 2
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
c chr2 3-10 + | 3 0.777777777777778
d chr2 4-10 * | 4 0.666666666666667
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
[1] NA 1 1 1 NA NA NA NA NA NA
[1] NA 2 2 2 NA NA NA NA NA NA
Hits object with 6 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 1 2
[2] 1 3
[3] 1 4
[4] 2 2
[5] 2 3
[6] 2 4
-------
queryLength: 2 / subjectLength: 10
Hits object with 2 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 1 4
[2] 2 3
-------
queryLength: 2 / subjectLength: 10
Hits object with 5 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 1 2
[2] 1 3
[3] 1 4
[4] 2 2
[5] 2 3
-------
queryLength: 2 / subjectLength: 10
Hits object with 0 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
-------
queryLength: 2 / subjectLength: 10
FALSE TRUE
7 3
a b c d e f g h i j
0 2 2 2 0 0 0 0 0 0
Hits object with 6 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 2 2
[2] 2 1
[3] 3 2
[4] 3 1
[5] 4 2
[6] 4 1
-------
queryLength: 10 / subjectLength: 2
GRanges object with 3 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
b chr2 2-10 + | 2 0.888888888888889
c chr2 3-10 + | 3 0.777777777777778
d chr2 4-10 * | 4 0.666666666666667
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
TRUE
3
gr1 gr2 gr3
3 2 2
Hits object with 7 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 1 2
[2] 1 3
[3] 1 4
[4] 2 5
[5] 2 6
[6] 3 1
[7] 3 4
-------
queryLength: 3 / subjectLength: 10
GRangesList object of length 3:
$gr1
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
[1] chr2 4-6 + | 5 0.45
[2] chr2 3-6 + | 4 0.45
$gr2
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
[1] chr1 7-9 + | 3 0.3
[2] chr1 13-15 - | 4 0.5
$gr3
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
[1] chr1 1-3 - | 6 0.4
[2] chr2 4-9 - | 2 0.1
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
gr1 gr2 gr3
2 0 2
Hits object with 4 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 1 4
[2] 1 3
[3] 3 1
[4] 3 4
-------
queryLength: 3 / subjectLength: 10
GRangesList object of length 2:
$gr1
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
[1] chr2 4-6 + | 5 0.45
[2] chr2 3-6 + | 4 0.45
$gr3
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
[1] chr1 1-3 - | 6 0.4
[2] chr2 4-9 - | 2 0.1
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
[1] 2 5 1
FALSE TRUE
2 1
gr1 gr2 gr3
2 0 0
Hits object with 2 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 1 2
[2] 1 1
-------
queryLength: 3 / subjectLength: 2
GRangesList object of length 1:
$gr1
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
[1] chr2 4-6 + | 5 0.45
[2] chr2 3-6 + | 4 0.45
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
gr1 gr2 gr3
2 0 0
Hits object with 2 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 1 1
[2] 1 2
-------
queryLength: 3 / subjectLength: 2
GRangesList object of length 1:
$gr1
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
[1] chr2 4-6 + | 5 0.45
[2] chr2 3-6 + | 4 0.45
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
[1] 1 NA NA
gr1 gr2 gr3
1 1 1
Hits object with 3 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 1 3
[2] 2 2
[3] 3 1
-------
queryLength: 3 / subjectLength: 3
GRangesList object of length 3:
$gr1
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
[1] chr2 4-6 + | 5 0.45
[2] chr2 3-6 + | 4 0.45
$gr2
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
[1] chr1 7-9 + | 3 0.3
[2] chr1 13-15 - | 4 0.5
$gr3
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
[1] chr1 1-3 - | 6 0.4
[2] chr2 4-9 - | 2 0.1
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
GenomicRanges documentation built on Nov. 8, 2020, 5:46 p.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
Various methods for finding/counting overlaps between objects containing genomic ranges. This man page describes the methods that operate on GenomicRanges and GRangesList objects.
NOTE: The findOverlaps generic function
and methods for IntegerRanges and
IntegerRangesList objects are defined and
documented in the IRanges package.
The methods for GAlignments,
GAlignmentPairs, and
GAlignmentsList objects are defined and
documented in the GenomicAlignments package.
GenomicRanges and GRangesList objects also support
countOverlaps, overlapsAny, and subsetByOverlaps
thanks to the default methods defined in the IRanges package and
to the findOverlaps and countOverlaps methods defined in
this package and documented below.
Usage
1 2 3 4 5 6 7 8 9 10 11 12 | ## S4 method for signature 'GenomicRanges,GenomicRanges'
findOverlaps(query, subject,
maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
select=c("all", "first", "last", "arbitrary"),
ignore.strand=FALSE)
## S4 method for signature 'GenomicRanges,GenomicRanges'
countOverlaps(query, subject,
maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
ignore.strand=FALSE)
|
Arguments
query, subject |
A GRanges or GRangesList object. |
maxgap, minoverlap, type |
See |
select |
When |
ignore.strand |
When set to |
Details
When the query and the subject are GRanges or
GRangesList objects, findOverlaps uses the triplet
(sequence name, range, strand) to determine which features (see
paragraph below for the definition of feature) from the query
overlap which features in the subject, where a strand value
of "*" is treated as occurring on both the "+" and
"-" strand.
An overlap is recorded when a feature in the query and a feature
in the subject have the same sequence name, have a compatible
pairing of strands (e.g. "+"/"+", "-"/"-",
"*"/"+", "*"/"-", etc.), and satisfy the
interval overlap requirements.
In the context of findOverlaps, a feature is a collection of
ranges that are treated as a single entity. For GRanges objects,
a feature is a single range; while for GRangesList objects,
a feature is a list element containing a set of ranges. In the results,
the features are referred to by number, which run from 1 to
length(query)/length(subject).
For type="equal" with GRangesList objects, query[[i]]
matches subject[[j]] iff for each range in query[[i]]
there is an identical range in subject[[j]], and vice versa.
Value
For findOverlaps either a Hits object when
select="all" or an integer vector otherwise.
For countOverlaps an integer vector containing the tabulated
query overlap hits.
Author(s)
P. Aboyoun, S. Falcon, M. Lawrence, and H. Pag<c3><a8>s
See Also
The Hits class for representing a set of hits between 2 vector-like objects.
The
findOverlapsgeneric function defined in the IRanges package.The GNCList constructor and class for preprocessing and representing a GenomicRanges or object as a data structure based on Nested Containment Lists.
The GRanges and GRangesList classes.
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 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 | ## ---------------------------------------------------------------------
## BASIC EXAMPLES
## ---------------------------------------------------------------------
## GRanges object:
gr <- GRanges(
seqnames=Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
ranges=IRanges(1:10, width=10:1, names=head(letters,10)),
strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
score=1:10,
GC=seq(1, 0, length=10)
)
gr
## GRangesList object:
gr1 <- GRanges(seqnames="chr2", ranges=IRanges(4:3, 6),
strand="+", score=5:4, GC=0.45)
gr2 <- GRanges(seqnames=c("chr1", "chr1"),
ranges=IRanges(c(7,13), width=3),
strand=c("+", "-"), score=3:4, GC=c(0.3, 0.5))
gr3 <- GRanges(seqnames=c("chr1", "chr2"),
ranges=IRanges(c(1, 4), c(3, 9)),
strand=c("-", "-"), score=c(6L, 2L), GC=c(0.4, 0.1))
grl <- GRangesList("gr1"=gr1, "gr2"=gr2, "gr3"=gr3)
## Overlapping two GRanges objects:
table(!is.na(findOverlaps(gr, gr1, select="arbitrary")))
countOverlaps(gr, gr1)
findOverlaps(gr, gr1)
subsetByOverlaps(gr, gr1)
countOverlaps(gr, gr1, type="start")
findOverlaps(gr, gr1, type="start")
subsetByOverlaps(gr, gr1, type="start")
findOverlaps(gr, gr1, select="first")
findOverlaps(gr, gr1, select="last")
findOverlaps(gr1, gr)
findOverlaps(gr1, gr, type="start")
findOverlaps(gr1, gr, type="within")
findOverlaps(gr1, gr, type="equal")
## ---------------------------------------------------------------------
## MORE EXAMPLES
## ---------------------------------------------------------------------
table(!is.na(findOverlaps(gr, gr1, select="arbitrary")))
countOverlaps(gr, gr1)
findOverlaps(gr, gr1)
subsetByOverlaps(gr, gr1)
## Overlaps between a GRanges and a GRangesList object:
table(!is.na(findOverlaps(grl, gr, select="first")))
countOverlaps(grl, gr)
findOverlaps(grl, gr)
subsetByOverlaps(grl, gr)
countOverlaps(grl, gr, type="start")
findOverlaps(grl, gr, type="start")
subsetByOverlaps(grl, gr, type="start")
findOverlaps(grl, gr, select="first")
table(!is.na(findOverlaps(grl, gr1, select="first")))
countOverlaps(grl, gr1)
findOverlaps(grl, gr1)
subsetByOverlaps(grl, gr1)
countOverlaps(grl, gr1, type="start")
findOverlaps(grl, gr1, type="start")
subsetByOverlaps(grl, gr1, type="start")
findOverlaps(grl, gr1, select="first")
## Overlaps between two GRangesList objects:
countOverlaps(grl, rev(grl))
findOverlaps(grl, rev(grl))
subsetByOverlaps(grl, rev(grl))
|
Example output
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
GRanges object with 10 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
a chr1 1-10 - | 1 1
b chr2 2-10 + | 2 0.888888888888889
c chr2 3-10 + | 3 0.777777777777778
d chr2 4-10 * | 4 0.666666666666667
e chr1 5-10 * | 5 0.555555555555556
f chr1 6-10 + | 6 0.444444444444444
g chr3 7-10 + | 7 0.333333333333333
h chr3 8-10 + | 8 0.222222222222222
i chr3 9-10 - | 9 0.111111111111111
j chr3 10 - | 10 0
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
FALSE TRUE
7 3
a b c d e f g h i j
0 2 2 2 0 0 0 0 0 0
Hits object with 6 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 2 2
[2] 2 1
[3] 3 2
[4] 3 1
[5] 4 2
[6] 4 1
-------
queryLength: 10 / subjectLength: 2
GRanges object with 3 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
b chr2 2-10 + | 2 0.888888888888889
c chr2 3-10 + | 3 0.777777777777778
d chr2 4-10 * | 4 0.666666666666667
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
a b c d e f g h i j
0 0 1 1 0 0 0 0 0 0
Hits object with 2 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 3 2
[2] 4 1
-------
queryLength: 10 / subjectLength: 2
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
c chr2 3-10 + | 3 0.777777777777778
d chr2 4-10 * | 4 0.666666666666667
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
[1] NA 1 1 1 NA NA NA NA NA NA
[1] NA 2 2 2 NA NA NA NA NA NA
Hits object with 6 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 1 2
[2] 1 3
[3] 1 4
[4] 2 2
[5] 2 3
[6] 2 4
-------
queryLength: 2 / subjectLength: 10
Hits object with 2 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 1 4
[2] 2 3
-------
queryLength: 2 / subjectLength: 10
Hits object with 5 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 1 2
[2] 1 3
[3] 1 4
[4] 2 2
[5] 2 3
-------
queryLength: 2 / subjectLength: 10
Hits object with 0 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
-------
queryLength: 2 / subjectLength: 10
FALSE TRUE
7 3
a b c d e f g h i j
0 2 2 2 0 0 0 0 0 0
Hits object with 6 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 2 2
[2] 2 1
[3] 3 2
[4] 3 1
[5] 4 2
[6] 4 1
-------
queryLength: 10 / subjectLength: 2
GRanges object with 3 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
b chr2 2-10 + | 2 0.888888888888889
c chr2 3-10 + | 3 0.777777777777778
d chr2 4-10 * | 4 0.666666666666667
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
TRUE
3
gr1 gr2 gr3
3 2 2
Hits object with 7 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 1 2
[2] 1 3
[3] 1 4
[4] 2 5
[5] 2 6
[6] 3 1
[7] 3 4
-------
queryLength: 3 / subjectLength: 10
GRangesList object of length 3:
$gr1
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
[1] chr2 4-6 + | 5 0.45
[2] chr2 3-6 + | 4 0.45
$gr2
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
[1] chr1 7-9 + | 3 0.3
[2] chr1 13-15 - | 4 0.5
$gr3
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
[1] chr1 1-3 - | 6 0.4
[2] chr2 4-9 - | 2 0.1
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
gr1 gr2 gr3
2 0 2
Hits object with 4 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 1 4
[2] 1 3
[3] 3 1
[4] 3 4
-------
queryLength: 3 / subjectLength: 10
GRangesList object of length 2:
$gr1
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
[1] chr2 4-6 + | 5 0.45
[2] chr2 3-6 + | 4 0.45
$gr3
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
[1] chr1 1-3 - | 6 0.4
[2] chr2 4-9 - | 2 0.1
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
[1] 2 5 1
FALSE TRUE
2 1
gr1 gr2 gr3
2 0 0
Hits object with 2 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 1 2
[2] 1 1
-------
queryLength: 3 / subjectLength: 2
GRangesList object of length 1:
$gr1
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
[1] chr2 4-6 + | 5 0.45
[2] chr2 3-6 + | 4 0.45
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
gr1 gr2 gr3
2 0 0
Hits object with 2 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 1 1
[2] 1 2
-------
queryLength: 3 / subjectLength: 2
GRangesList object of length 1:
$gr1
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
[1] chr2 4-6 + | 5 0.45
[2] chr2 3-6 + | 4 0.45
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
[1] 1 NA NA
gr1 gr2 gr3
1 1 1
Hits object with 3 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 1 3
[2] 2 2
[3] 3 1
-------
queryLength: 3 / subjectLength: 3
GRangesList object of length 3:
$gr1
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
[1] chr2 4-6 + | 5 0.45
[2] chr2 3-6 + | 4 0.45
$gr2
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
[1] chr1 7-9 + | 3 0.3
[2] chr1 13-15 - | 4 0.5
$gr3
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | score GC
[1] chr1 1-3 - | 6 0.4
[2] chr2 4-9 - | 2 0.1
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
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