GPos-class {GenomicRanges} | R Documentation

## Memory-efficient representation of genomic positions

### Description

The GPos class is a container for storing a set of genomic positions where most of the positions are typically (but not necessarily) adjacent. Because genomic positions can be seen as genomic ranges of width 1, the GPos class extends the GenomicRanges virtual class. Note that even though a GRanges instance can be used for storing genomic positions, using a GPos object will be much more memory-efficient, especially when the object contains long runs of adjacent positions in ascending order.

### Usage

    GPos(pos_runs)  # constructor function

### Arguments

`pos_runs` | A GRanges object (or any other GenomicRanges derivative) where each range is interpreted as a run of adjacent ascending genomic positions on the same strand. If `pos_runs` is not a GenomicRanges derivative, `GPos()` first tries to coerce it to one with `as(pos_runs, "GenomicRanges", strict=FALSE)`.

### Value

A GPos object.

### Accessors

#### Getters

GPos objects support the same set of getters as other GenomicRanges derivatives (i.e. `seqnames()`, `ranges()`, `start()`, `end()`, `strand()`, `mcols()`, `seqinfo()`, etc...), plus the `pos()` getter which is equivalent to `start()` or `end()`. See `?GenomicRanges` for the list of getters supported by GenomicRanges derivatives.

IMPORTANT NOTES:

1. `ranges()` returns an IPos object instead of the IRanges object that one gets with other GenomicRanges derivatives. To get an IRanges object, you need to call `ranges()` again on the IPos object i.e. do `ranges(ranges(x))`) on GPos object `x`.

2. Note that a GPos object cannot hold names i.e. `names()` always returns `NULL` on it.

#### Setters

Like GRanges objects, GPos objects support the following setters:

- The `seqnames()` and `strand()` setters.

- The `mcols()` and `metadata()` setters.

- The family of setters that operate on the seqinfo component of an object: `seqlevels()`, `seqlevelsStyle()`, `seqlengths()`, `isCircular()`, `genome()`, and `seqinfo()`. These setters are defined and documented in the GenomeInfoDb package.

However, there is no `pos()` setter for GPos objects at the moment (although one might be added in the future).

### Coercion

From GenomicRanges to GPos: A GenomicRanges derivative `x` in which all the ranges have a width of 1 can be coerced to a GPos object with `as(x, "GPos")`. The names on `x` are not propagated (a warning is issued if `x` has names on it).

From GPos to GRanges: A GPos object `x` can be coerced to a GRanges object with `as(x, "GRanges")`. However be aware that the resulting object can use thousands times (or more) memory than `x`! See "MEMORY USAGE" in the Examples section below.

From GPos to ordinary R objects: Like with any other GenomicRanges derivative, `as.character()`, `as.factor()`, and `as.data.frame()` work on a GPos object `x`. Note however that `as.data.frame(x)` returns a data frame with a `pos` column (containing `pos(x)`) instead of the `start`, `end`, and `width` columns that one gets with other GenomicRanges derivatives.

### Subsetting

A GPos object can be subsetted exactly like a GRanges object.

### Concatenation

GPos objects can be concatenated together with `c()` or `append()`.

### Splitting and Relisting

Like with any other GRanges object, `split()` and `relist()` work on a GPos object.

### Note

Like for any Vector derivative, the length of a GPos object cannot exceed `.Machine$integer.max` (i.e. 2^31 on most platforms). `GPos()` will return an error if `pos_runs` contains too many genomic positions.

Internal representation of GPos objects has changed in GenomicRanges 1.29.10 (Bioc 3.6). Update any old object `x` with: `x <- updateObject(x, verbose=TRUE)`.

### Author(s)

Hervé Pagès; based on ideas borrowed from Georg Stricker georg.stricker@in.tum.de and Julien Gagneur gagneur@in.tum.de

### See Also

- The IPos class in the IRanges package for a memory-efficient representation of integer positions (i.e. integer ranges of width 1).

- GenomicRanges and GRanges objects.

- The `seqinfo` accessor and family in the GenomeInfoDb package for accessing/modifying the seqinfo component of an object.

- GenomicRanges-comparison for comparing and ordering genomic positions.

- findOverlaps-methods for finding overlapping genomic ranges and/or positions.

- nearest-methods for finding the nearest genomic range/position neighbor.

- The `snpsBySeqname`, `snpsByOverlaps`, and `snpsById` methods for SNPlocs objects defined in the BSgenome package for extractors that return a GPos object.

- SummarizedExperiment objects in the SummarizedExperiment package.

### Examples

    ## ---------------------------------------------------------------------
    ## BASIC EXAMPLES
    ## ---------------------------------------------------------------------

    ## Example 1:
    gpos1 <- GPos(c("chr1:44-53", "chr1:5-10", "chr2:2-5"))
    gpos1

    length(gpos1)
    seqnames(gpos1)
    pos(gpos1)  # same as 'start(gpos1)' and 'end(gpos1)'
    strand(gpos1)
    as.character(gpos1)
    as.data.frame(gpos1)
    as(gpos1, "GRanges")
    as.data.frame(as(gpos1, "GRanges"))
    gpos1[9:17]

    ## Example 2:
    pos_runs <- GRanges("chrI", IRanges(c(1, 6, 12, 17), c(5, 10, 16, 20)),
                        strand=c("+", "-", "-", "+"))
    gpos2 <- GPos(pos_runs)
    gpos2

    strand(gpos2)

    ## Example 3:
    gpos3A <- gpos3B <- GPos(c("chrI:1-1000", "chrI:1005-2000"))
    npos <- length(gpos3A)

    mcols(gpos3A)$sample <- Rle("sA")
    sA_counts <- sample(10, npos, replace=TRUE)
    mcols(gpos3A)$counts <- sA_counts

    mcols(gpos3B)$sample <- Rle("sB")
    sB_counts <- sample(10, npos, replace=TRUE)
    mcols(gpos3B)$counts <- sB_counts

    gpos3 <- c(gpos3A, gpos3B)
    gpos3

    ## Example 4:
    library(BSgenome.Scerevisiae.UCSC.sacCer2)
    genome <- BSgenome.Scerevisiae.UCSC.sacCer2
    gpos4 <- GPos(seqinfo(genome))
    gpos4  # all the positions along the genome are represented
    mcols(gpos4)$dna <- do.call("c", unname(as.list(genome)))
    gpos4

    ## Note however that, like for any Vector derivative, the length of a
    ## GPos object cannot exceed '.Machine$integer.max' (i.e. 2^31 on most
    ## platforms) so the above only works with a "small" genome.
    ## For example it doesn't work with the Human genome:
    library(TxDb.Hsapiens.UCSC.hg19.knownGene)
    ## Not run:
      GPos(seqinfo(TxDb.Hsapiens.UCSC.hg19.knownGene))  # error!

    ## End(Not run)

    ## You can use isSmallGenome() to check upfront whether the genome is
    ## "small" or not.
    isSmallGenome(genome)
    isSmallGenome(TxDb.Hsapiens.UCSC.hg19.knownGene)

    ## ---------------------------------------------------------------------
    ## MEMORY USAGE
    ## ---------------------------------------------------------------------

    ## Coercion to GRanges works...
    gr4 <- as(gpos4, "GRanges")
    gr4
    ## ... but is generally not a good idea:
    object.size(gpos4)
    object.size(gr4)  # 8 times bigger than the GPos object!

    ## Shuffling the order of the positions impacts memory usage:
    gpos4r <- rev(gpos4)
    object.size(gpos4r)  # significantly
    gpos4s <- sample(gpos4)
    object.size(gpos4s)  # even worse!

    ## AN IMPORTANT NOTE: In the worst situations, GPos still performs as
    ## good as a GRanges object.
    object.size(as(gpos4r, "GRanges"))  # same size as 'gpos4r'
    object.size(as(gpos4s, "GRanges"))  # same size as 'gpos4s'

    ## Best case scenario is when the object is strictly sorted (i.e.
    ## positions are in strict ascending order).
    ## This can be checked with:
    is.unsorted(gpos4, strict=TRUE)  # 'gpos4' is strictly sorted

    ## ---------------------------------------------------------------------
    ## USING MEMORY-EFFICIENT METADATA COLUMNS
    ## ---------------------------------------------------------------------
    ## In order to keep memory usage as low as possible, it is recommended
    ## to use a memory-efficient representation of the metadata columns that
    ## we want to set on the object. Rle's are particularly well suited for
    ## this, especially if the metadata columns contain long runs of
    ## identical values. This is the case for example if we want to use a
    ## GPos object to represent the coverage of sequencing reads along a
    ## genome.

    ## Example 5:
    library(pasillaBamSubset)
    library(Rsamtools)  # for the BamFile() constructor function
    bamfile1 <- BamFile(untreated1_chr4())
    bamfile2 <- BamFile(untreated3_chr4())
    gpos5 <- GPos(seqinfo(bamfile1))
    library(GenomicAlignments)  # for "coverage" method for BamFile objects
    cvg1 <- unlist(coverage(bamfile1), use.names=FALSE)
    cvg2 <- unlist(coverage(bamfile2), use.names=FALSE)
    mcols(gpos5) <- DataFrame(cvg1, cvg2)
    gpos5

    object.size(gpos5)  # lightweight

    ## Keep only the positions where coverage is at least 10 in one of the
    ## 2 samples:
    gpos5[mcols(gpos5)$cvg1 >= 10 | mcols(gpos5)$cvg2 >= 10]

    ## ---------------------------------------------------------------------
    ## USING A GPos OBJECT IN A SummarizedExperiment OBJECT
    ## ---------------------------------------------------------------------
    ## Because the GPos class extends the GenomicRanges virtual class, a GPos
    ## object can be used as the rowRanges component of a SummarizedExperiment
    ## object.

    ## As a 1st example, we show how the counts for samples sA and sB in
    ## 'gpos3' can be stored in a SummarizedExperiment object where the rows
    ## correspond to unique genomic positions and the columns to samples:
    library(SummarizedExperiment)
    counts <- cbind(sA=sA_counts, sB=sB_counts)
    mcols(gpos3A) <- NULL
    rse3 <- SummarizedExperiment(list(counts=counts), rowRanges=gpos3A)
    rse3
    rowRanges(rse3)
    head(assay(rse3))

    ## Finally we show how the coverage data from Example 5 can be easily
    ## stored in a lightweight SummarizedExperiment object:
    cvg <- mcols(gpos5)
    mcols(gpos5) <- NULL
    rse5 <- SummarizedExperiment(list(cvg=cvg), rowRanges=gpos5)
    rse5
    rowRanges(rse5)
    assay(rse5)

    ## Keep only the positions where coverage is at least 10 in one of the
    ## 2 samples:
    rse5[assay(rse5)$cvg1 >= 10 | assay(rse5)$cvg2 >= 10]

[Package GenomicRanges version 1.36.1 Index]