GenomicRanges-comparison: Comparing and ordering genomic ranges

In vjcitn/GenomicRangesGHA: Representation and manipulation of genomic intervals; demo with github actions binary generation

Description

Methods for comparing and/or ordering GenomicRanges objects.

Usage

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

## S4 method for signature 'GenomicRanges'
duplicated(x, incomparables=FALSE, fromLast=FALSE,
           nmax=NA, 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("auto", "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", "last", "random", "max", "min"),
     ignore.strand=FALSE)

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

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

Arguments

x, table, y	GenomicRanges objects.
incomparables	Not supported.
fromLast, method, nomatch, nmax, na.rm, strictly, na.last, decreasing	See ?`IPosRanges-comparison` in the IRanges package for a description of these arguments.
ignore.strand	Whether or not the strand should be ignored when comparing 2 genomic ranges.
...	One or more GenomicRanges objects. The GenomicRanges objects after the first one are used to break ties.
ties.method	A character string specifying how ties are treated. Only "first" is supported for now.
by	An optional formula that is resolved against as.env(x); the resulting variables are passed to order to generate the ordering permutation.

Details

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

The "natural order" for the elements of a GenomicRanges derivative 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, because we already do (c) and (d) for regular ranges (see ?`IPosRanges-comparison`), genomic ranges that belong to the same underlying sequence and strand are ordered like regular ranges.

pcompare(), ==, !=, <=, >=, < and > on GenomicRanges derivatives behave accordingly to this "natural order".

is.unsorted(), order(), sort(), rank() on GenomicRanges derivatives also behave accordingly to this "natural order".

Finally, note that some inter range transformations like reduce or disjoin also use this "natural order" implicitly when operating on GenomicRanges derivatives.

Author(s)

H. Pagès, is.unsorted contributed by Pete Hickey

See Also

• The GenomicRanges class.

• IPosRanges-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. match(), selfmatch(), %in%, duplicated(), unique()
## ---------------------------------------------------------------------
table <- gr[1:7]
match(gr, table)
match(gr, table, ignore.strand=TRUE)

gr %in% table

duplicated(gr)
unique(gr)

## ---------------------------------------------------------------------
## C. 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)

## ---------------------------------------------------------------------
## D. 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, ties.method="first")
rank(gr, ties.method="first", ignore.strand=TRUE)

## ---------------------------------------------------------------------
## E. 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))

vjcitn/GenomicRangesGHA documentation built on Jan. 18, 2021, 12:39 a.m.