inst/scripts/Exp2_R10_prot.R

In samWieczorek/DAPARdata: Data accompanying the DAPAR and Prostar packages

library("MSnbase")
library("DAPAR")

exprsFile <- system.file("extdata", "Exp2_R10_prot.txt", package="DAPARdata")

metadataFile <- system.file("extdata", "samples_Exp2_R10.txt", package="DAPARdata")
metadata <- read.table(metadataFile, header=TRUE, sep="\t", as.is=TRUE)

Exp2_R10_prot <- createMSnset(file = exprsFile, 
                              metadata = metadata, 
                              indExpData = 1:6, 
                              colnameForID = 'id',
                              indexForMetacell = 43:48,
                              logData = TRUE, 
                              replaceZeros = TRUE,
                              pep_prot_data = "protein",
                              proteinId = "Protein_IDs",
                              software = 'maxquant')