MaxQprotein {DDPNA}

read proteomic quantification data and seperate the protein information and quantification information.

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

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)