GAlignmentsList-class {GenomicAlignments} | R Documentation

## GAlignmentsList objects

### Description

The GAlignmentsList class is a container for storing a collection of GAlignments objects.

### Details

A GAlignmentsList object contains a list of GAlignments objects. The majority of operations on this page are described in more detail on the GAlignments man page, see ?`GAlignments`.

### Constructor

  `GAlignmentsList(...)`: Creates a GAlignmentsList from a list of GAlignments objects.

### Accessors

In the code snippets below, `x` is a GAlignmentsList object.

  `length(x)`: Return the number of elements in `x`.

  `names(x)`, `names(x) <- value`: Get or set the names of the elements of `x`.

  `seqnames(x)`, `seqnames(x) <- value`: Get or set the name of the reference sequences of the alignments in each element of `x`.

  `rname(x)`, `rname(x) <- value`: Same as `seqnames(x)` and `seqnames(x) <- value`.

  `strand(x)`, `strand(x) <- value`: Get or set the strand of the alignments in each element of `x`.

  `cigar(x)`: Returns a character list of length `length(x)` containing the CIGAR string for the alignments in each element of `x`.

  `qwidth(x)`: Returns an integer list of length `length(x)` containing the length of the alignments in each element of `x` *after* hard clipping (i.e. the length of the query sequence that is stored in the corresponding SAM/BAM record).

  `start(x)`, `end(x)`: Returns an integer list of length `length(x)` containing the "start" and "end" (respectively) of the alignments in each element of `x`.

  `width(x)`: Returns an integer list of length `length(x)` containing the "width" of the alignments in each element of `x`.

  `njunc(x)`: Returns an integer list of length `x` containing the number of junctions (i.e. N operations in the CIGAR) for the alignments in each element of `x`.

  `seqinfo(x)`, `seqinfo(x) <- value`: Get or set the information about the underlying sequences. `value` must be a Seqinfo object.

  `seqlevels(x)`, `seqlevels(x) <- value`: Get or set the sequence levels of the alignments in each element of `x`.

  `seqlengths(x)`, `seqlengths(x) <- value`: Get or set the sequence lengths for each element of `x`. `seqlengths(x)` is equivalent to `seqlengths(seqinfo(x))`. `value` can be a named non-negative integer or numeric vector eventually with NAs.

  `isCircular(x)`, `isCircular(x) <- value`: Get or set the circularity flags for the alignments in each element in `x`. `value` must be a named logical list eventually with NAs.

  `genome(x)`, `genome(x) <- value`: Get or set the genome identifier or assembly name for the alignments in each element of `x`. `value` must be a named character list eventually with NAs.

  `seqnameStyle(x)`: Get or set the seqname style for alignments in each element of `x`.

### Coercion

In the code snippets below, `x` is a GAlignmentsList object.

  `granges(x, use.names=TRUE, use.mcols=FALSE, ignore.strand=FALSE)`, `ranges(x, use.names=TRUE, use.mcols=FALSE)`:

  Return either a GRanges or a IRanges object of length `length(x)`. Note this coercion IGNORES the cigar information. The resulting ranges span the entire range, including any junctions or spaces between paired-end reads.

  If `use.names` is TRUE, then the names on `x` (if any) are propagated to the returned object. If `use.mcols` is TRUE, then the metadata columns on `x` (if any) are propagated to the returned object.

  `granges` coercion supports `ignore.strand` to allow ranges of opposite strand to be combined (see examples). All ranges in the resulting GRanges will have strand ‘*’.

  `grglist(x, use.names=TRUE, use.mcols=FALSE, ignore.strand=FALSE)`, `rglist(x, use.names=TRUE, use.mcols=FALSE)`:

  Return either a GRangesList or an IRangesList object of length `length(x)`. This coercion RESPECTS the cigar information. The resulting ranges are fragments of the original ranges that do not include junctions or spaces between paired-end reads.

  If `use.names` is TRUE, then the names on `x` (if any) are propagated to the returned object. If `use.mcols` is TRUE, then the metadata columns on `x` (if any) are propagated to the returned object.

  `grglist` coercion supports `ignore.strand` to allow ranges of opposite strand to be combined (see examples). When `ignore.strand` is TRUE all ranges in the resulting GRangesList have strand ‘*’.

  `as(x, "GRanges")`, `as(x, "IntegerRanges")`, `as(x, "GRangesList")`, `as(x, "IntegerRangesList")`: Alternate ways of doing `granges(x, use.names=TRUE, use.mcols=TRUE)`, `ranges(x, use.names=TRUE, use.mcols=TRUE)`, `grglist(x, use.names=TRUE, use.mcols=TRUE)`, and `rglist(x, use.names=TRUE, use.mcols=TRUE)`, respectively.

  `as.data.frame(x, row.names = NULL, optional = FALSE, ..., value.name = "value", use.outer.mcols = FALSE, group_name.as.factor = FALSE)`: Coerces `x` to a `data.frame`. See as.data.frame on the `List` man page for details (?`List`).

  `as(x, "GALignmentsList")`: Here `x` is a GAlignmentPairs object. Return a GAlignmentsList object of length `length(x)` where the i-th list element represents the ranges of the i-th alignment pair in `x`.

### Subsetting and related operations

In the code snippets below, `x` is a GAlignmentsList object.

  `x[i]`, `x[i] <- value`: Get or set list elements `i`. `i` can be a numeric or logical vector. `value` must be a GAlignments.

  `x[[i]]`, `x[[i]] <- value`: Same as `x[i]`, `x[i] <- value`.

  `x[i, j]`, `x[i, j] <- value`: Get or set list elements `i` with optional metadata columns `j`. `i` can be a numeric, logical or missing. `value` must be a GAlignments.

### Concatenation

  `c(x, ..., ignore.mcols=FALSE)`: Concatenate GAlignmentsList object `x` and the GAlignmentsList objects in `...` together. See `?c` in the S4Vectors package for more information about concatenating Vector derivatives.

### Author(s)

Valerie Obenchain <Valerie.Obenchain@RoswellPark.org>

### References

http://samtools.sourceforge.net/

### See Also

- `readGAlignmentsList` for reading genomic alignments from a file (typically a BAM file) into a GAlignmentsList object.

- GAlignments and GAlignmentPairs objects for handling aligned single- and paired-end reads, respectively.

- junctions-methods for extracting and summarizing junctions from a GAlignmentsList object.

- findOverlaps-methods for finding range overlaps between a GAlignmentsList object and another range-based object.

- `seqinfo` in the GenomeInfoDb package for getting/setting/modifying the sequence information stored in an object.

- The GRanges and GRangesList classes defined and documented in the GenomicRanges package.

### Examples

    gal1 <- GAlignments(
        seqnames=Rle(factor(c("chr1", "chr2", "chr1", "chr3")),
            c(1, 3, 2, 4)),
        pos=1:10, cigar=paste0(10:1, "M"),
        strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
        names=head(letters, 10), score=1:10)

    gal2 <- GAlignments(
        seqnames=Rle(factor(c("chr2", "chr4")), c(3, 4)), pos=1:7,
        cigar=c("5M", "3M2N3M2N3M", "5M", "10M", "5M1N4M", "8M2N1M", "5M"),
        strand=Rle(strand(c("-", "+")), c(4, 3)),
        names=tail(letters, 7), score=1:7)

    galist <- GAlignmentsList(noGaps=gal1, Gaps=gal2)

    ## ---------------------------------------------------------------------
    ## A. BASIC MANIPULATION
    ## ---------------------------------------------------------------------

    length(galist)
    names(galist)
    seqnames(galist)
    strand(galist)
    head(cigar(galist))
    head(qwidth(galist))
    head(start(galist))
    head(end(galist))
    head(width(galist))
    head(njunc(galist))
    seqlevels(galist)

    ## Rename the reference sequences:
    seqlevels(galist) <- sub("chr", "seq", seqlevels(galist))
    seqlevels(galist)

    grglist(galist)  # a GRangesList object
    rglist(galist)   # an IRangesList object

    ## ---------------------------------------------------------------------
    ## B. SUBSETTING
    ## ---------------------------------------------------------------------

    galist[strand(galist) == "-"]
    has_junctions <- sapply(galist,
                            function(x) any(grepl("N", cigar(x), fixed=TRUE)))
    galist[has_junctions]

    ## Different ways to subset:
    galist[2]             # a GAlignments object of length 1
    galist[[2]]           # a GAlignments object of length 1
    grglist(galist[2])  # a GRangesList object of length 1
    rglist(galist[2])   # a NormalIRangesList object of length 1

    ## ---------------------------------------------------------------------
    ## C. mcols()/elementMetadata()
    ## ---------------------------------------------------------------------

    ## Metadata can be defined on the individual GAlignment elements
    ## and the overall GAlignmentsList object. By default, 'level=between'
    ## extracts the GALignmentsList metadata. Using 'level=within'
    ## will extract the metadata on the individual GAlignments objects.

    mcols(galist) ## no metadata on the GAlignmentsList object
    mcols(galist, level="within")

    ## ---------------------------------------------------------------------
    ## D. readGAlignmentsList()
    ## ---------------------------------------------------------------------

    library(pasillaBamSubset)

    ## 'file' as character.
    fl <- untreated3_chr4()
    galist1 <- readGAlignmentsList(fl)

    galist1[1:3]
    length(galist1)
    table(elementNROWS(galist1))

    ## When 'file' is a BamFile, 'asMates' must be TRUE. If FALSE,
    ## the data are treated as single-end and each list element of the
    ## GAlignmentsList will be of length 1. For single-end data
    ## use readGAlignments() instead of readGAlignmentsList().
    bf <- BamFile(fl, yieldSize=3, asMates=TRUE)
    readGAlignmentsList(bf)

    ## Use a 'param' to fine tune the results.
    param <- ScanBamParam(flag=scanBamFlag(isProperPair=TRUE))
    galist2 <- readGAlignmentsList(fl, param=param)
    length(galist2)

    ## ---------------------------------------------------------------------
    ## E. COERCION
    ## ---------------------------------------------------------------------

    ## The granges() and grlist() coercions support 'ignore.strand' to
    ## allow ranges from different strands to be combined. In this example
    ## paired-end reads aligned to opposite strands were read into a
    ## GAlignmentsList. If the desired operation is to combine these ranges,
    ## regardless of junctions or the space between pairs, 'ignore.strand'
    ## must be TRUE.
    granges(galist[1])
    granges(galist[1], ignore.strand=TRUE)

    ## grglist()
    galist <- GAlignmentsList(noGaps=gal1, Gaps=gal2)
    grglist(galist)
    grglist(galist, ignore.strand=TRUE)

[Package GenomicAlignments version 1.24.0 Index]