Proteins-class: Proteins class.

In vladpetyuk/simMSnSet: Simulation of MSnSet Objects

Description

Details about Proteins class.

Usage

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

## S4 method for signature 'Proteins'
simulate(object, seed = NULL)

Arguments

object	Proteins-class object
seed	an integer for set.seed

Details

Class holding the information about the proteins and peptides

Methods (by generic)

• show: Show method for a Proteins object

• simulate: Simulates the number of peptides per protein (if not provided) and ionization efficiencies of each peptide.

Slots

nProt

number of proteins

fdrPeptide

FDR of peptide identifications

fdrMatching

FDR of peptide to spectrum or LC-MS feature matching

propChanging

proportion of proteins that are changed between the different phenotype groups. At this point it is independent of phenotype groups. It shoud, however, depend on phenotype.

changingProtIdx

index indicating which proteins are changing

nPep

number of peptides

lambda

parameter of Poisson distribution controlling the number of peptides per protein during the simulation

meanIoinizationIntensity

a numeric value of mean peptide intensity

noise

measurement noise. So far one value for all. May be in the future convert to signal/noise ratio.

pepCounts

integer vector with number of peptides per each protein

protNames

character vector with generated protein names

pepNames

character vector with generacted peptide names

ionizationEff

numeric vector with simulated ionization efficiencies for the peptides

missThreshAbsolute

soft threshold in absolute intensity. It has precedence over missThreshQuantile.

missThreshQuantile

quantile to determine soft threshold value.

missThreshSharpness

parameter controlling the sharpness of the thresholding step function. The suggested interval for the sharpness values is [2,100]. At 2 it approximates linear (not necessarily the best setting). At 100 it is almost a step-function. The suggested values are >5.

features

data.frame containing peptide and protein names

Examples

pr <- Proteins(nProt=10)
pr <- simulate(pr)
show(pr)

vladpetyuk/simMSnSet documentation built on May 3, 2019, 6:16 p.m.