aggregateHifly: Protein aggregate function using hifly method
In bartongroup/Proteus: Downstream analysis of the MaxQuant output

aggregateHifly

R Documentation

Protein aggregate function using hifly method

Description

Function to aggregate peptides into proteins using a hi-flyer method of Silva et al. 2006 (http://www.mcponline.org/content/5/1/144.full.pdf).

Usage

aggregateHifly(wp, hifly = 3)

Arguments

`wp`	Intensity table with selection of peptides for this protein
`hifly`	Number of high-fliers

Details

This function should be used from within makeProteinTable. The "hifly" method is a follows.

For a given protein find all corresponding peptides.
In each replicate, order intensities from the highest to the lowest. This is done separately for each replicate.
Select n top rows of the ordered table.
In each replicate, find the mean of these three rows. This is the estimated protein intensity.

Value

A numeric vector with aggregated protein intensities

Examples

## Not run: 
library(proteusLabelFree)
data(proteusLabelFree)
prodat <- makeProteinTable(pepdat.clean, aggregate.fun=aggregateHifly, hifly=3)

## End(Not run)

bartongroup/Proteus documentation built on April 22, 2023, 5:33 a.m.