MaxQprotein: read proteomic quantification data and seperate the protein...

In liukf10/TEST: Disease-Drived Differential Proteins and Proteome-Wide Co-Expression Network Associated Analysis

Description

The function will seperate data into 4 parts: protein information, intensity, iBAQ and LFQ (iBAQ and LFQ only fit for MaxQuant software result). For MaxQ data, it can remove the contaminant and reverse protein.

Usage

MaxQprotein(proteinGroups, IDname = "Majority.protein.IDs",
            IDtype = "MaxQ", remove = TRUE, QuanCol = NULL,
            verbose = 1)

Arguments

proteinGroups	the proteomic quantification data
IDname	The column name of uniprot ID. The default value is "Majority.protein.IDs"" which is the column name in MaxQuant data.
IDtype	"MaxQ" means proteinGroups is Maxquant quantification data, "none" means other type data. This must be (an abbreviation of) one of the strings: "MaxQ","none".
remove	a logical value indicated whether remove contaminant and reverse ID.
QuanCol	The quantification data columns. It's only needed when IDtype is "none". When IDtype is "none" and QuanCol is not given, the intensity will auto extract all columns except IDname as quantification data. It may have error in next analysis.
verbose	integer level of verbosity. Zero means silent, 1 means have Diagnostic Messages.

Value

a list of proteomic information.

protein_IDs	Portein IDs which is IDname column information.
intensity	Quantification intensity informaton. When IDtype is "none", it is the QuanCol columns information.
iBAQ	Quantification iBAQ intensity informaton.(only for IDtype is "MaxQ")
LFQ	Quantification LFQ intensity informaton.(only for IDtype is "MaxQ")

Author(s)

Kefu Liu

Examples

rm(list = ls())
library(DDPNA)
data(ProteomicData)
# example for MaxQ Data
MaxQdata <- MaxQprotein(ProteomicData$MaxQ)
# example for other type Data
otherdata <- MaxQprotein(ProteomicData$none, IDname = "Protein",
                         IDtype = "none", QuanCol = 2:9)

liukf10/TEST documentation built on May 20, 2019, 12:59 a.m.