makeProteinTable: Make protein table

In bartongroup/Proteus: Downstream analysis of the MaxQuant output

Make protein table

Description

makeProteinTable creates a protein table from the peptide table. Protein intensities or ratios are aggregated from peptide data. An external function is used to aggregate each protein.

Usage

makeProteinTable(
  pepdat,
  aggregate.fun = aggregateHifly,
  ...,
  min.peptides = 2,
  ncores = 4
)

Arguments

pepdat	A proteusData object containing peptide data, normally created by makePeptideTable
aggregate.fun	Function to aggregate peptides into a protein. See "Details" for more details.
...	Additional parameters to pass to aggregate.fun
min.peptides	Minimum number of peptides per protein
ncores	Number of cores for parallel processing

Details

There are three protein aggregation functions provided in this package: aggregateHifly, aggregateMedian and aggregateSum. Depending on the needs, the user can provide any arbitrary function to perform aggregation.

The aggregate function should be in form: function(wp, ...). wp is a matrix containing measurements from all peptides for the particular protein. Rows are peptides, columns are samples. ... are additional parameters for the function that are passed from makeProteinTable. The aggregate function should return a vector of values for each sample. That is the length of the vector should be the same as the number of columns in wp.

Value

A proteusData object containing protein intensities and metadata.

Examples

library(proteusLabelFree)
data(proteusLabelFree)
prodat <- makeProteinTable(pepdat.clean, ncores=2)

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