## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( fig.width=7, fig.height=4.5, collapse = TRUE, eval = TRUE, comment = "#>" ) ## ----------------------------------------------------------------------------- library(ComPrAn) inputFile <- system.file("extData", "data.txt", package = "ComPrAn") #read in data peptides <- peptideImport(inputFile) #mandatory filtering peptides <- cleanData(peptides, fCol = "Search ID") #optional filtering peptides <- toFilter(peptides, rank = 1) # separate chemical modifications and labelling into separate columns peptides <- splitModLab(peptides) #remove unnecessary columns, simplify rows peptides <- simplifyProteins(peptides) ## ----------------------------------------------------------------------------- peptide_index <- pickPeptide(peptides) ## ----------------------------------------------------------------------------- protein <- "P52815" max_frac <- 23 #example all peptide plot (default settings) allPeptidesPlot(peptide_index,protein, max_frac = max_frac) ## ----------------------------------------------------------------------------- listOnlyOneLabState <- onlyInOneLabelState(peptide_index) ## ----------------------------------------------------------------------------- # produce a data frame in a format needed for downstream analysis forAnalysis <- getNormTable(peptide_index,purpose = "analysis") # produce a data frame in an easily human readable format that can be exported forExport <- getNormTable(peptide_index,purpose = "export")