FragmentViews-class {topdownr} | R Documentation

## The FragmentViews class

### Description

The FragmentViews class is a basic container for storing a set of views (start/end locations) on the same peptides/protein sequence. Additionally it keeps information about mass, type and charge of the fragments.

### Usage

    FragmentViews(
      sequence,
      mass,
      type,
      z = 1L,
      start = NULL,
      end = NULL,
      width = NULL,
      names = NULL,
      metadata = list()
    )

    ## S4 method for signature 'FragmentViews,FragmentViews'
    combine(x, y)

    ## S4 method for signature 'FragmentViews'
    mz(object, ...)

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

### Arguments

`sequence` | `character`/ Biostrings::AAString, complete protein/peptide sequence.
`mass` | `double`, mass of the fragments, same length as `start`/`end`/`width`.
`type` | `character`, type of the fragments, same length as `start`/`end`/width'.
`z` | `integer`, charge of the fragments, length one or same length as `start`/`end`/width'.
`start` | `integer`, start positions of the fragments. At least two of `start`/`end`/width' has to be given.
`end` | `integer`, end positions of the fragments. At least two of `start`/`end`/width' has to be given.
`width` | `integer`, width positions of the fragments. At least two of `start`/`end`/width' has to be given.
`names` | `character`, names of the fragments, same length as `start`/`end`/width'.
`metadata` | `list`, metadata like modifications.
`object, x, y` | FragmentViews
`...` | arguments passed to internal/other methods.

### Details

FragmentViews extends Biostrings::XStringViews. In short it combines an IRanges::IRanges object to store start/end location on a sequence, an Biostrings::AAString object.

### Value

An FragmentViews object.

### Functions

- `FragmentViews`: Constructor

  In general it is not necessary to call the constructor manually. See `readTopDownFiles()` instead.

### Coercion

`as(object, "data.frame")`: Coerce an FragmentViews object into a `data.frame`.

### Author(s)

Sebastian Gibb mail@sebastiangibb.de

### See Also

Biostrings::XStringViews

### Examples

    # Constructor
    fv <- FragmentViews("ACE", start=1, width=1:3, names=paste0("b", 1:3),
                        mass=c(72.04439, 232.07504, 361.11763),
                        type="b", z=1)
    fv

    # Coercion to data.frame
    as(fv, "data.frame")
    as(fv, "data.frame")

[Package topdownr version 1.12.0 Index]