renewable {ShortRead} | R Documentation

## Renew (update) a ShortRead object with new values

### Description

Use `renew` to update an object defined in ShortRead with new values. Discover update-able classes and values with `renewable`.

### Usage

    renewable(x, ...)
    renew(x, ...)

### Arguments

`x` | For `renewable`: `missing`, `character(1)`, or a class defined in the ShortRead package. For `renew`: an instance of a class defined in the ShortRead package.
`...` | For `renewable`, ignored. For `renew`, named arguments identifying which parts of `x` are to be renewed.

### Details

When invoked with no arguments `renewable` returns a character vector naming classes that can be renewed.

When invoked with a `character(1)` or an instance of a ShortRead class, a list of the names and values of the elements that can be renewed. When `x` is a character vector naming a virtual class, then each element of the returned list is a non-virtual descendant of that class that can be used in renewal. This is not fully recursive.

`renew` is always invoked with the `x` argument being an instance of a class identified by `renewable()`. Remaining arguments are name-value pairs identifying the components of `x` that are to be renewed (updated). The name-value pairs must be consistent with `renewable(x)`. The resulting object is checked for validity. Multiple components of the object can be updated in a single call to `renew`, allowing comparatively efficient complex transformations.

### Value

`renewable()` returns a character vector of renewable classes.

`renewable(x)` returns a named list. The names correspond to renewable classes, and the elements of the list correspond to renewable components of the class.

`renew(x, ...)` returns an object of the same class as `x`, but with components of `x` replaced by the named values of `...`.

### Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

### Examples

    ## discovery
    renewable()
    renewable("AlignedRead")
    renewable("QualityScore") ## instantiable classes

    ## example data
    sp <- SolexaPath(system.file("extdata", package="ShortRead"))
    ap <- analysisPath(sp)
    filt <- chromosomeFilter("chr[[:digit:]+].fa")
    aln <- readAligned(ap, "s_2_export.txt", "SolexaExport",
                       filter=filt)

    ## renew chromosomes from 'chr1.fa' to 'chr1', etc
    labels <- sub("\\.fa", "", levels(chromosome(aln)))
    renew(aln, chromosome=factor(chromosome(aln), labels=labels))

    ## multiple changes -- update chromosome, offset position
    renew(aln, chromosome=factor(chromosome(aln), labels=labels),
          position=1L+position(aln))

    ## oops! invalid instances cannot be constructed
    try(renew(aln, position=1:10))

[Package ShortRead version 1.45.4 Index]