## ----startup, results='hide', echo=FALSE, message=FALSE----------------------- library(mzID) ps.options(pointsize=12) ## ----parsing, tidy=TRUE------------------------------------------------------- exampleFiles <- list.files(system.file('extdata', package = 'mzID'), pattern = '*.mzid', full.names = TRUE) mzResults <- mzID(exampleFiles[5]) mzResults ## ----class_overview, tidy=TRUE------------------------------------------------ showClass('mzID') ## ----flattening, tidy=TRUE---------------------------------------------------- flatResults <- flatten(mzResults) names(flatResults) nrow(flatResults) #The length of an mzID object is the number of PSM's length(mzResults) ## ----inspection, tidy=TRUE---------------------------------------------------- flatResults$length nchar(flatResults$sequence) substr(flatResults$sequence, 1, 10)