## ----style, eval=TRUE, echo=FALSE, results="asis"------------------------ BiocStyle::latex() ## ----knitr, include=FALSE, cache=FALSE----------------------------------- library("knitr") suppressPackageStartupMessages(library("MSnbase")) suppressPackageStartupMessages(library("pRolocdata")) opts_chunk$set(fig.align = 'center', fig.show = 'hold', par = TRUE, prompt = TRUE, comment = NA) options(replace.assign = TRUE, width = 70) ## ----readCsvData0, tidy = FALSE------------------------------------------ ## 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, tidy = FALSE------------------------------------------ ## 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, tidy = FALSE-------------------------------------------- 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) ## ----label=sessioninfo,results='asis',echo=FALSE,cache=FALSE------------- toLatex(sessionInfo())