Description Usage Arguments Value Author(s) Examples
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.
1 2 3 | MaxQprotein(proteinGroups, IDname = "Majority.protein.IDs",
IDtype = "MaxQ", remove = TRUE, QuanCol = NULL,
verbose = 1)
|
proteinGroups |
the proteomic quantification data |
IDname |
The column name of uniprot ID. The default value is " |
IDtype |
" |
remove |
a logical value indicated whether remove contaminant and reverse ID. |
QuanCol |
The quantification data columns. It's only needed when |
verbose |
integer level of verbosity. Zero means silent, 1 means have Diagnostic Messages. |
a list of proteomic information.
protein_IDs |
Portein IDs which is |
intensity |
Quantification intensity informaton. When |
iBAQ |
Quantification iBAQ intensity informaton.(only for |
LFQ |
Quantification LFQ intensity informaton.(only for |
Kefu Liu
1 2 3 4 5 6 7 8 | 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)
|
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