pepAgregate {DAPAR}R Documentation

Function agregate peptides to proteins

Description

Method to agregate with a method peptides to proteins on a MSnSet object (peptides)

Usage

pepAgregate(obj.pep, protID, method = "sum overall", matAdj = NULL,
  n = NULL)

Arguments

obj.pep

An object (peptides) of class MSnSet.

protID

The name of proteins ID column

method

The method used to aggregate the peptides into proteins. Values are "sum", "mean" or "sum on top n" : do the sum / mean of intensity on all peptides belonging to proteins. Default is "sum"

matAdj

An adjacency matrix

n

The number of peptides considered for the aggregation.

Value

An object of class MSnSet with proteins

Author(s)

Alexia Dorffer, Samuel Wieczorek

Examples

require(DAPARdata)
data(Exp1_R25_pept)
protID <- "Protein.group.IDs"
mat <- BuildAdjacencyMatrix(Exp1_R25_pept[1:1000], protID, TRUE)
pepAgregate(Exp1_R25_pept[1:1000], protID, "sum overall", mat)

[Package DAPAR version 1.10.4 Index]