## ----style, echo = FALSE, results = 'asis', message=FALSE--------------------- BiocStyle::markdown() ## ---- echo = FALSE, message = FALSE------------------------------------------- library(Spectra) library(BiocStyle) ## ---- eval = FALSE------------------------------------------------------------ # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("MsBackendMgf") ## ----load-libs---------------------------------------------------------------- library(Spectra) library(MsBackendMgf) fls <- dir(system.file("extdata", package = "MsBackendMgf"), full.names = TRUE, pattern = "mgf$") fls ## ----import------------------------------------------------------------------- library(BiocParallel) register(SerialParam()) sps <- Spectra(fls, source = MsBackendMgf()) ## ----spectravars-------------------------------------------------------------- spectraVariables(sps) ## ----instrument--------------------------------------------------------------- sps$rtime sps$TITLE ## ----spectravariables--------------------------------------------------------- spectraVariableMapping(MsBackendMgf()) ## ----map---------------------------------------------------------------------- map <- c(spectrumName = "TITLE", spectraVariableMapping(MsBackendMgf())) map ## ----import2------------------------------------------------------------------ sps <- Spectra(fls, source = MsBackendMgf(), mapping = map) ## ----spectrumName------------------------------------------------------------- sps$spectrumName ## ----mz----------------------------------------------------------------------- mz(sps) intensity(sps) ## ----export------------------------------------------------------------------- fl <- tempfile() export(sps, backend = MsBackendMgf(), file = fl, mapping = map) ## ----export-check------------------------------------------------------------- readLines(fl)[1:12] ## ----------------------------------------------------------------------------- sps$new_variable <- "A" export(sps, backend = MsBackendMgf(), file = fl) readLines(fl)[1:12] ## ----------------------------------------------------------------------------- sps_ex <- selectSpectraVariables(sps, c("mz", "intensity", "rtime", "acquisitionNum", "precursorMz", "precursorCharge")) export(sps_ex, backend = MsBackendMgf(), file = fl, exportTitle = FALSE) readLines(fl)[1:12] ## ----------------------------------------------------------------------------- sessionInfo()