transformMSstatsToMSnSet {MSstats} | R Documentation |
Convert the required input format for MSstats into general format (MSnSet class in MSnbase package) on the proteomics.
transformMSstatsToMSnSet(data)
data |
name of the raw (input) data set with required column for MSstats. |
raw : See SRMRawData
for the required data structure of raw (input) data.
output : After transformation, assayData includes value of Intensity. phenoData has variables of IsotopeLabelType, Condition, BioReplicate,Run. featureData has variables of ProteinName, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge.
Ching-Yun Chang, Meena Choi, Olga Vitek.
Maintainer: Meena Choi (mnchoi67@gmail.com)
Meena Choi, Ching-Yun Chang, Timothy Clough, Daniel Broudy, Trevor Killeen, Brendan MacLean and Olga Vitek. "MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments" Bioinformatics, 30(17):2524-2526, 2014.
Ching-Yun Chang, Paola Picotti, Ruth Huttenhain, Viola Heinzelmann-Schwarz, Marko Jovanovic, Ruedi Aebersold, Olga Vitek. "Protein significance analysis in selected reaction monitoring (SRM) measurements." Molecular & Cellular Proteomics, 11:M111.014662, 2012.
Timothy Clough, Safia Thaminy, Susanne Ragg, Ruedi Aebersold, Olga Vitek. "Statistical protein quantification and significance analysis in label-free LC-M experiments with complex designs" BMC Bioinformatics, 13:S16, 2012.
Gatto, L. and Lilly, K.S. (2012). MSnbase-an R Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation. Bioinformatics, 28, 288-289.
library(MSnbase) quant.msnset<-transformMSstatsToMSnSet(SRMRawData)