CTSS-class {CAGEr} | R Documentation

## CAGE Transcription Start Sites

### Description

The `CTSS` class represents CAGE transcription start sites (CTSS) at single-nucleotide resolution, using `GenomicRanges::UnstitchedGPos` as base class. It is used by CAGEr for type safety.

The `CTSS` constructor takes the same arguments as `GenomicRanges::GPos`, plus `bsgenomeName`, and minus `stitch`, which is hardcoded to `FALSE`.

The `CTSS.chr` class represents a `CTSS` object that is guaranteed to be only on a single chromosome. It is used internally by CAGEr for type-safe polymorphic dispatch.

### Usage

    ## S4 method for signature 'CTSS'
    show(object)

    ## S4 method for signature 'CTSS'
    initialize(.Object, ..., bsgenomeName = NULL)

    CTSS(
      seqnames = NULL,
      pos = NULL,
      strand = NULL,
      ...,
      seqinfo = NULL,
      seqlengths = NULL,
      bsgenomeName = NULL
    )

    ## S4 method for signature 'CTSS,GRanges'
    coerce(from, to = "GRanges", strict = TRUE)

    ## S4 method for signature 'GRanges,CTSS'
    coerce(from, to = "CTSS", strict = TRUE)

### Arguments

`object` | See `methods::show`
`.Object` | See `methods::new`
`bsgenomeName` | String containing the name of a BSgenome package.
`seqnames, pos, strand, seqinfo, seqlengths, ...` | See the documentation of `GenomicRanges::GPos` for further details.
`from, to, strict` | See `methods::coerce`.

### Details

The `genomeName` element of the `metadata` slot is used to store the name of the BSgenome package used when constructing the `CAGEr` object.

Coercion from `GRanges` to `CTSS` loses information, but it seems to be fine, since other coercions like `as(1.2, "integer")` do the same.

### Author(s)

Charles Plessy

### Examples

    # Convert an UnstitchedGPos object using the new() constructor.
    gp <- GPos("chr1:2:-", stitch = FALSE)
    ctss <- new("CTSS", gp, bsgenomeName = "BSgenome.Drerio.UCSC.danRer7")
    genomeName(ctss)

    # Create a new object using the CTSS() constructor.
    CTSS("chr1", 2, "-", bsgenomeName = "BSgenome.Drerio.UCSC.danRer7")

    # Coerce CTSS to GRanges
    as(ctss, "GRanges")

    # Coerce a GRanges object to CTSS using the as() method.
    gr <- GRanges("chr1:1-10:-")
    gr$seq <- "AAAAAAAAAA"
    seqlengths(gr) <- 100
    genome(gr) <- "foo"
    as(gr, "CTSS")
    identical(seqinfo(gr), seqinfo(as(gr, "CTSS")))
    as(as(gr, "CTSS"), "CTSS") # Make sure it works twice in a row

    # (internal use) Transform CTSS to CTSS.chr object
    ctss.chr <- as(CTSScoordinatesGR(exampleCAGEexp), "CTSS.chr")

[Package CAGEr version 2.0.2 Index]