## ----style, echo = FALSE, results = 'asis', message=FALSE--------------------- BiocStyle::markdown() ## ----echo = FALSE, message = FALSE-------------------------------------------- library(MsExperiment) library(Spectra) library(BiocStyle) ## ----load_pkg, message = FALSE------------------------------------------------ library("MsExperiment") ## ----load_spectra, message = FALSE-------------------------------------------- library("Spectra") ## ----px, eval = TRUE---------------------------------------------------------- library("rpx") px <- PXDataset("PXD022816") px pxfiles(px) ## ----fls, eval = TRUE--------------------------------------------------------- (i <- grep(".+0[12].+mzML$", pxfiles(px), value = TRUE)) fls <- pxget(px, i) fls ## ----make_exp, eval = TRUE---------------------------------------------------- msexp <- MsExperiment() msexp ## ----make_exp_fls, eval = TRUE------------------------------------------------ msfls <- MsExperimentFiles(mzmls = fls, fasta = "homo_sapiens.fasta") msfls ## ----add_exp_fls, eval = TRUE------------------------------------------------- experimentFiles(msexp) <- msfls msexp ## ----add_sample_data, eval = TRUE--------------------------------------------- sampleData(msexp) <- DataFrame( mzmls = basename(experimentFiles(msexp)[["mzmls"]]), fractions = 1:2) sampleData(msexp) ## ----sp, eval = TRUE---------------------------------------------------------- sp <- Spectra(experimentFiles(msexp)[["mzmls"]]) sp ## ----add_sp, eval = TRUE------------------------------------------------------ spectra(msexp) <- sp msexp ## ----make_cmd, eval = TRUE---------------------------------------------------- mzids <- sub("mzML", "mzid", basename(experimentFiles(msexp)[["mzmls"]])) paste0("java -jar /path/to/MSGFPlus.jar", " -s ", experimentFiles(msexp)[["mzmls"]], " -o ", mzids, " -d ", experimentFiles(msexp)[["fasta"]], " -t 20ppm", " -m 0", " int 1") ## ----touch, eval = TRUE------------------------------------------------------- (output <- file.path(tempdir(), mzids)) cmd <- paste("touch", output) cmd ## ----system, eval = TRUE------------------------------------------------------ sapply(cmd, system) ## ----add_mzids, eval = TRUE--------------------------------------------------- experimentFiles(msexp)[["mzids"]] <- mzids experimentFiles(msexp) msexp ## ----add_cmd, eval = TRUE----------------------------------------------------- metadata(msexp)[["mzmls_to_mzids"]] <- cmd metadata(msexp) ## ----exp_exists, eval = TRUE-------------------------------------------------- existMsExperimentFiles(msexp) ## ----save_exp, eval = TRUE---------------------------------------------------- saveRDS(msexp, "msexp.rds") rm(list = ls()) ## ----read_exp, eval = TRUE---------------------------------------------------- msexp <- readRDS("msexp.rds") msexp experimentFiles(msexp) ## ----plot_sp, eval = TRUE----------------------------------------------------- sp <- spectra(msexp) sp plotSpectra(sp[1000]) ## ----make_exp2---------------------------------------------------------------- lmse <- MsExperiment() sd <- DataFrame(sample_id = c("QC1", "QC2"), sample_name = c("QC Pool", "QC Pool"), injection_idx = c(1, 3)) sampleData(lmse) <- sd ## ----add_fls2----------------------------------------------------------------- fls <- dir(system.file("sciex", package = "msdata"), full.names = TRUE) basename(fls) experimentFiles(lmse) <- MsExperimentFiles( mzML_files = fls, annotations = "internal_standards.txt") ## ----add_sp2------------------------------------------------------------------ sps <- Spectra(fls, backend = MsBackendMzR()) spectra(lmse) <- sps lmse ## ----link_sample_data--------------------------------------------------------- lmse <- linkSampleData(lmse, with = "experimentFiles.mzML_file", sampleIndex = c(1, 2), withIndex = c(1, 2)) ## ----echo = FALSE------------------------------------------------------------- knitr::include_graphics("imgs/Links_01.png") ## ----link_sample_data2-------------------------------------------------------- lmse <- linkSampleData(lmse, with = "experimentFiles.annotations", sampleIndex = c(1, 2), withIndex = c(1, 1)) ## ----echo = FALSE------------------------------------------------------------- knitr::include_graphics("imgs/Links_02.png") ## ----link_sample_data3-------------------------------------------------------- sampleData(lmse)$raw_file <- normalizePath(fls) lmse <- linkSampleData( lmse, with = "sampleData.raw_file = spectra.dataOrigin") ## ----show_link---------------------------------------------------------------- sampleData(lmse)$raw_file head(spectra(lmse)$dataOrigin) ## ----echo = FALSE------------------------------------------------------------- knitr::include_graphics("imgs/Links_03.png") ## ----show_exp2---------------------------------------------------------------- lmse ## ----add_se, message = FALSE-------------------------------------------------- library(SummarizedExperiment) sd <- DataFrame(sample = c("QC2", "QC1", "QC3"), idx = c(3, 1, 5)) se <- SummarizedExperiment(colData = sd, assay = cbind(1:10, 11:20, 21:30)) qdata(lmse) <- se ## ----link_sample_data4-------------------------------------------------------- sampleData(lmse)$sample_id qdata(lmse)$sample lmse <- linkSampleData(lmse, with = "sampleData.sample_id = qdata.sample") lmse ## ----subset_exp2-------------------------------------------------------------- b <- lmse[2] b ## ----extract_exp2------------------------------------------------------------- assay(qdata(b)) ## ----add_metadata------------------------------------------------------------- metadata(lmse)$other <- data.frame(sample_name = c("study_1", "POOL", "study_2"), index = 1:3) b <- lmse[2] metadata(b) ## ----link_sample_data5-------------------------------------------------------- lmse <- linkSampleData(lmse, with = "metadata.other", sampleIndex = 1:2, withIndex = c(2, 2)) b <- lmse[2] metadata(b) ## ----show_subset_exp2--------------------------------------------------------- lmse <- lmse[c(2, 1)] sampleData(lmse) ## ----show_expfls2_msml-------------------------------------------------------- experimentFiles(lmse)$mzML_file ## ----show_explfs2_annot------------------------------------------------------- experimentFiles(lmse)$annotations ## ----si----------------------------------------------------------------------- sessionInfo()