FragmentViews-class: The FragmentViews class

In sgibb/topdownr: Investigation of Fragmentation Conditions in Top-Down Proteomics

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 [e-mail]

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")

sgibb/topdownr documentation built on Jan. 16, 2024, 12:14 a.m.