Comparing and ordering genomic ranges

Description

Methods for comparing and ordering the elements in one or more GenomicRanges objects.

Usage

## duplicated()
## ------------

## S4 method for signature 'GenomicRanges'
duplicated(x, incomparables=FALSE, fromLast=FALSE,
           method=c("auto", "quick", "hash"))

## match() & selfmatch()
## ---------------------

## S4 method for signature 'GenomicRanges,GenomicRanges'
match(x, table, nomatch=NA_integer_, incomparables=NULL,
      method=c("auto", "quick", "hash"), ignore.strand=FALSE)

## S4 method for signature 'GenomicRanges'
selfmatch(x, method=c("auto", "quick", "hash"), ignore.strand=FALSE)

## order() and related methods
## ----------------------------

## S4 method for signature 'GenomicRanges'
is.unsorted(x, na.rm=FALSE, strictly=FALSE, ignore.strand=FALSE)

## S4 method for signature 'GenomicRanges'
order(..., na.last=TRUE, decreasing=FALSE, method=c("shell", "radix"))

## S4 method for signature 'GenomicRanges'
sort(x, decreasing=FALSE, ignore.strand=FALSE, by)

## S4 method for signature 'GenomicRanges'
rank(x, na.last=TRUE,
     ties.method=c("average", "first", "random", "max", "min"))

## Generalized parallel comparison of 2 GenomicRanges objects
## ----------------------------------------------------------

## S4 method for signature 'GenomicRanges,GenomicRanges'
pcompare(x, y)

Arguments

Details

Two elements of a GenomicRanges object (i.e. two genomic ranges) are considered equal iff they are on the same underlying sequence and strand, and have the same start and width. duplicated() and unique() on a GenomicRanges object are conforming to this.

The "natural order" for the elements of a GenomicRanges object is to order them (a) first by sequence level, (b) then by strand, (c) then by start, (d) and finally by width. This way, the space of genomic ranges is totally ordered. Note that the reduce method for GenomicRanges uses this "natural order" implicitly. Also, note that, because we already do (c) and (d) for regular ranges (see ?`Ranges-comparison`), genomic ranges that belong to the same underlying sequence and strand are ordered like regular ranges.

is.unsorted(), order(), sort(), and rank() on a GenomicRanges object behave accordingly to this "natural order".

==, !=, <=, >=, < and > on GenomicRanges objects also behave accordingly to this "natural order".

Author(s)

H. Pag<c3><83><c2><a8>s, is.unsorted contributed by Pete Hickey

See Also

• The GenomicRanges class.

• Ranges-comparison in the IRanges package for comparing and ordering genomic ranges.

• findOverlaps-methods for finding overlapping genomic ranges.

• intra-range-methods and inter-range-methods for intra range and inter range transformations of a GRanges object.

• setops-methods for set operations on GenomicRanges objects.

Examples

gr0 <- GRanges(
    Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
    IRanges(c(1:9,7L), end=10),
    strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
    seqlengths=c(chr1=11, chr2=12, chr3=13)
)
gr <- c(gr0, gr0[7:3])
names(gr) <- LETTERS[seq_along(gr)]

## ---------------------------------------------------------------------
## A. ELEMENT-WISE (AKA "PARALLEL") COMPARISON OF 2 GenomicRanges OBJECTS
## ---------------------------------------------------------------------
gr[2] == gr[2]  # TRUE
gr[2] == gr[5]  # FALSE
gr == gr[4]
gr >= gr[3]

## ---------------------------------------------------------------------
## B. duplicated(), unique()
## ---------------------------------------------------------------------
duplicated(gr)
unique(gr)

## ---------------------------------------------------------------------
## C. match(), %in%
## ---------------------------------------------------------------------
table <- gr[1:7]
match(gr, table)
match(gr, table, ignore.strand=TRUE)

gr %in% table

## ---------------------------------------------------------------------
## D. findMatches(), countMatches()
## ---------------------------------------------------------------------
findMatches(gr, table)
countMatches(gr, table)

findMatches(gr, table, ignore.strand=TRUE)
countMatches(gr, table, ignore.strand=TRUE)

gr_levels <- unique(gr)
countMatches(gr_levels, gr)

## ---------------------------------------------------------------------
## E. order() AND RELATED METHODS
## ---------------------------------------------------------------------
is.unsorted(gr)
order(gr)
sort(gr)
is.unsorted(sort(gr))

is.unsorted(gr, ignore.strand=TRUE)
gr2 <- sort(gr, ignore.strand=TRUE)
is.unsorted(gr2)  # TRUE
is.unsorted(gr2, ignore.strand=TRUE)  # FALSE

## TODO: Broken. Please fix!
#sort(gr, by = ~ seqnames + start + end) # equivalent to (but slower than) above

score(gr) <- rev(seq_len(length(gr)))

## TODO: Broken. Please fix!
#sort(gr, by = ~ score)

rank(gr)

## ---------------------------------------------------------------------
## F. GENERALIZED ELEMENT-WISE COMPARISON OF 2 GenomicRanges OBJECTS
## ---------------------------------------------------------------------
gr3 <- GRanges(c(rep("chr1", 12), "chr2"), IRanges(c(1:11, 6:7), width=3))
strand(gr3)[12] <- "+"
gr4 <- GRanges("chr1", IRanges(5, 9))

pcompare(gr3, gr4)
rangeComparisonCodeToLetter(pcompare(gr3, gr4))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GenomicRanges)
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, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GenomicRanges/GenomicRanges-comparison.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GenomicRanges-comparison
> ### Title: Comparing and ordering genomic ranges
> ### Aliases: GenomicRanges-comparison pcompare
> ###   pcompare,GenomicRanges,GenomicRanges-method
> ###   duplicated,GenomicRanges-method duplicated.GenomicRanges
> ###   match,GenomicRanges,GenomicRanges-method
> ###   selfmatch,GenomicRanges-method is.unsorted,GenomicRanges-method
> ###   order,GenomicRanges-method sort,GenomicRanges-method
> ###   sort.GenomicRanges rank,GenomicRanges-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> gr0 <- GRanges(
+     Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
+     IRanges(c(1:9,7L), end=10),
+     strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
+     seqlengths=c(chr1=11, chr2=12, chr3=13)
+ )
> gr <- c(gr0, gr0[7:3])
> names(gr) <- LETTERS[seq_along(gr)]
> 
> ## ---------------------------------------------------------------------
> ## A. ELEMENT-WISE (AKA "PARALLEL") COMPARISON OF 2 GenomicRanges OBJECTS
> ## ---------------------------------------------------------------------
> gr[2] == gr[2]  # TRUE
[1] TRUE
> gr[2] == gr[5]  # FALSE
[1] FALSE
> gr == gr[4]
 [1] FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[13] FALSE  TRUE FALSE
> gr >= gr[3]
 [1] FALSE FALSE  TRUE  TRUE FALSE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE
[13] FALSE  TRUE  TRUE
> 
> ## ---------------------------------------------------------------------
> ## B. duplicated(), unique()
> ## ---------------------------------------------------------------------
> duplicated(gr)
 [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE
[13]  TRUE  TRUE  TRUE
> unique(gr)
GRanges object with 10 ranges and 0 metadata columns:
    seqnames    ranges strand
       <Rle> <IRanges>  <Rle>
  A     chr1   [1, 10]      -
  B     chr2   [2, 10]      +
  C     chr2   [3, 10]      +
  D     chr2   [4, 10]      *
  E     chr1   [5, 10]      *
  F     chr1   [6, 10]      +
  G     chr3   [7, 10]      +
  H     chr3   [8, 10]      +
  I     chr3   [9, 10]      -
  J     chr3   [7, 10]      -
  -------
  seqinfo: 3 sequences from an unspecified genome
> 
> ## ---------------------------------------------------------------------
> ## C. match(), %in%
> ## ---------------------------------------------------------------------
> table <- gr[1:7]
> match(gr, table)
 [1]  1  2  3  4  5  6  7 NA NA NA  7  6  5  4  3
> match(gr, table, ignore.strand=TRUE)
 [1]  1  2  3  4  5  6  7 NA NA  7  7  6  5  4  3
> 
> gr %in% table
 [1]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE  TRUE  TRUE
[13]  TRUE  TRUE  TRUE
> 
> ## ---------------------------------------------------------------------
> ## D. findMatches(), countMatches()
> ## ---------------------------------------------------------------------
> findMatches(gr, table)
Hits object with 12 hits and 0 metadata columns:
       queryHits subjectHits
       <integer>   <integer>
   [1]         1           1
   [2]         2           2
   [3]         3           3
   [4]         4           4
   [5]         5           5
   ...       ...         ...
   [8]        11           7
   [9]        12           6
  [10]        13           5
  [11]        14           4
  [12]        15           3
  -------
  queryLength: 15 / subjectLength: 7
> countMatches(gr, table)
 [1] 1 1 1 1 1 1 1 0 0 0 1 1 1 1 1
> 
> findMatches(gr, table, ignore.strand=TRUE)
Hits object with 13 hits and 0 metadata columns:
       queryHits subjectHits
       <integer>   <integer>
   [1]         1           1
   [2]         2           2
   [3]         3           3
   [4]         4           4
   [5]         5           5
   ...       ...         ...
   [9]        11           7
  [10]        12           6
  [11]        13           5
  [12]        14           4
  [13]        15           3
  -------
  queryLength: 15 / subjectLength: 7
> countMatches(gr, table, ignore.strand=TRUE)
 [1] 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1
> 
> gr_levels <- unique(gr)
> countMatches(gr_levels, gr)
 [1] 1 1 2 2 2 2 2 1 1 1
> 
> ## ---------------------------------------------------------------------
> ## E. order() AND RELATED METHODS
> ## ---------------------------------------------------------------------
> is.unsorted(gr)
[1] TRUE
> order(gr)
 [1]  6 12  1  5 13  2  3 15  4 14  7 11  8 10  9
> sort(gr)
GRanges object with 15 ranges and 0 metadata columns:
    seqnames    ranges strand
       <Rle> <IRanges>  <Rle>
  F     chr1   [6, 10]      +
  L     chr1   [6, 10]      +
  A     chr1   [1, 10]      -
  E     chr1   [5, 10]      *
  M     chr1   [5, 10]      *
  .      ...       ...    ...
  G     chr3   [7, 10]      +
  K     chr3   [7, 10]      +
  H     chr3   [8, 10]      +
  J     chr3   [7, 10]      -
  I     chr3   [9, 10]      -
  -------
  seqinfo: 3 sequences from an unspecified genome
> is.unsorted(sort(gr))
[1] FALSE
> 
> is.unsorted(gr, ignore.strand=TRUE)
[1] TRUE
> gr2 <- sort(gr, ignore.strand=TRUE)
> is.unsorted(gr2)  # TRUE
[1] TRUE
> is.unsorted(gr2, ignore.strand=TRUE)  # FALSE
[1] FALSE
> 
> ## TODO: Broken. Please fix!
> #sort(gr, by = ~ seqnames + start + end) # equivalent to (but slower than) above
> 
> score(gr) <- rev(seq_len(length(gr)))
> 
> ## TODO: Broken. Please fix!
> #sort(gr, by = ~ score)
> 
> rank(gr)
 [1]  3  6  7  9  4  1 11 13 15 14 12  2  5 10  8
> 
> ## ---------------------------------------------------------------------
> ## F. GENERALIZED ELEMENT-WISE COMPARISON OF 2 GenomicRanges OBJECTS
> ## ---------------------------------------------------------------------
> gr3 <- GRanges(c(rep("chr1", 12), "chr2"), IRanges(c(1:11, 6:7), width=3))
> strand(gr3)[12] <- "+"
> gr4 <- GRanges("chr1", IRanges(5, 9))
> 
> pcompare(gr3, gr4)
 [1]  -6  -5  -4  -4  -1   2   3   4   4   5   6 -11  42
> rangeComparisonCodeToLetter(pcompare(gr3, gr4))
 [1] a b c c f i j k k l m X X
Levels: a b c d e f g h i j k l m X
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>