## ----env, echo=FALSE------------------------------------------------------- suppressPackageStartupMessages(library("BiocStyle")) suppressPackageStartupMessages(library("MSnbase")) suppressPackageStartupMessages(library("pRolocdata")) ## ----include_forword, echo=FALSE, results="asis"--------------------------- cat(readLines("./Foreword.md"), sep = "\n") ## ----include_bugs, echo=FALSE, results="asis"------------------------------ cat(readLines("./Bugs.md"), sep = "\n") ## ----readCsvData0---------------------------------------------------------- ## The original data for replicate 1, available ## from the pRolocdata package f0 <- dir(system.file("extdata", package = "pRolocdata"), full.names = TRUE, pattern = "pr800866n_si_004-rep1.csv") csv <- read.csv(f0) ## ----showOrgCsv------------------------------------------------------------ head(csv, n=3) ## ----readCsvData1---------------------------------------------------------- ## The quantitation data, from the original data f1 <- dir(system.file("extdata", package = "pRolocdata"), full.names = TRUE, pattern = "exprsFile.csv") exprsCsv <- read.csv(f1) ## Feature meta-data, from the original data f2 <- dir(system.file("extdata", package = "pRolocdata"), full.names = TRUE, pattern = "fdataFile.csv") fdataCsv <- read.csv(f2) ## Sample meta-data, a new file f3 <- dir(system.file("extdata", package = "pRolocdata"), full.names = TRUE, pattern = "pdataFile.csv") pdataCsv <- read.csv(f3) ## ----showExprsFile--------------------------------------------------------- head(exprsCsv, n = 3) ## ----showFdFile------------------------------------------------------------ head(fdataCsv, n = 3) ## ----showPdFile------------------------------------------------------------ pdataCsv ## ----makeMSnSet------------------------------------------------------------ library("MSnbase") res <- readMSnSet(exprsFile = f1, featureDataFile = f2, phenoDataFile = f3, sep = ",") res ## ----readMSnSet2----------------------------------------------------------- ecol <- paste("area", 114:117, sep = ".") fname <- "Protein.ID" eset <- readMSnSet2(f0, ecol, fname) eset ## ----ecols----------------------------------------------------------------- getEcols(f0, ",") grepEcols(f0, "area", ",") e <- grepEcols(f0, "area", ",") readMSnSet2(f0, e) ## -------------------------------------------------------------------------- sessionInfo()