FragmentViews-class {topdownr} | R Documentation |
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.
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)
sequence |
|
mass |
|
type |
|
z |
|
start |
|
end |
|
width |
|
names |
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metadata |
|
object, x, y |
FragmentViews |
... |
arguments passed to internal/other methods. |
FragmentViews extends Biostrings::XStringViews. In short it combines an IRanges::IRanges object to store start/end location on a sequence, an Biostrings::AAString object.
An FragmentViews object.
FragmentViews
: Constructor
In general it is not necessary to call the constructor manually. See
readTopDownFiles()
instead.
as(object, "data.frame")
: Coerce an
FragmentViews object into a data.frame
.
Sebastian Gibb mail@sebastiangibb.de
# 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")