## ----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("MsBackendMsp") ## ----message = FALSE---------------------------------------------------------- library(MsBackendMsp) nist <- system.file("extdata", "spectrum2.msp", package = "MsBackendMsp") ## ----------------------------------------------------------------------------- sp <- Spectra(nist, source = MsBackendMsp()) ## ----spectravars-------------------------------------------------------------- spectraVariables(sp) ## ----------------------------------------------------------------------------- sp$msLevel sp$name sp$adduct ## ----------------------------------------------------------------------------- spectraVariableMapping(MsBackendMsp()) ## ----------------------------------------------------------------------------- mona <- system.file("extdata", "minimona.msp", package = "MsBackendMsp") head(readLines(mona)) ## ----------------------------------------------------------------------------- head(readLines(nist)) ## ----------------------------------------------------------------------------- spectraVariableMapping(MsBackendMsp(), "mona") ## ----------------------------------------------------------------------------- sp_mona <- Spectra(mona, source = MsBackendMsp(), mapping = spectraVariableMapping(MsBackendMsp(), "mona")) sp_mona$precursorMz ## ----------------------------------------------------------------------------- sp_mona[29:30]$synonym ## ----------------------------------------------------------------------------- tmpf <- tempfile() export(sp_mona, backend = MsBackendMsp(), file = tmpf, mapping = spectraVariableMapping(MsBackendMsp())) head(readLines(tmpf)) ## ----------------------------------------------------------------------------- tmpf <- tempfile() export(sp, backend = MsBackendMsp(), file = tmpf, mapping = spectraVariableMapping(MsBackendMsp(), "mona")) head(readLines(tmpf)) ## ----------------------------------------------------------------------------- sessionInfo()