transformMSstatsToMSnSet: Transformation input format for MSstats to MSnSet class

Description

Convert the required input format for MSstats into general format (MSnSet class in MSnbase package) on the proteomics.

Usage

transformMSstatsToMSnSet(data)

Arguments

data

name of the raw (input) data set with required column for MSstats.

Details

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.

References

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.

Examples

Run this code

	
library(MSnbase)
quant.msnset<-transformMSstatsToMSnSet(SRMRawData)

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