protiq (version 1.2)

scampi-class: Class "scampi"

Description

This class of objects is used to group the input data for various functions in the protiq package. It is not needed to run the main functions such as runScampi and iterateScampi (which return objects of the class scampiVal). However, it is needed to run "under-functions" such as quantifyProteins. Objects of this class have methods for the functions summary, show and plot.

Creation of objects

Objects are created e.g. by new("scampi", peptides, proteins, edgespp).

Slots

peptides:

Object of class "data.frame": dataframe summarizing information about the peptides (input data as well as (optionally) reassessed abundances).

proteins:

Object of class "data.frame": dataframe summarizing information about the proteins (input data as well as estimated protein abundances).

edgespp:

Object of class "data.frame": dataframe summarizing the information about the edges of ppGraph, connecting the peptides to the proteins.

Methods

plot

signature(x = "scampi", y = "missing"): Plot the distribution of the measured peptide abundances (histogram).

show

signature(object = "scampi"): Display basic properties of the fitted object.

summary

signature(object = "scampi"): Display details of the fitted object.

Examples

showClass("scampi")

## generate a scampi object
data("leptoSRM")
scampiData <- scampi(peptides=leptoSRMpeptides, 
                     proteins=leptoSRMproteins, 
                     edgespp=leptoSRMedgespp)

## use methods of class scampiVal
show(scampiData)
summary(scampiData)
plot(scampiData)