## ----style, eval=TRUE, echo=FALSE, results="asis"------------------------ BiocStyle::latex() ## ----openraw------------------------------------------------------------- library(mzR) library(msdata) mzxml <- system.file("threonine/threonine_i2_e35_pH_tree.mzXML", package = "msdata") aa <- openMSfile(mzxml) ## ramp, default backend ## ----get header information---------------------------------------------- runInfo(aa) instrumentInfo(aa) header(aa,1) ## ----plotspectrum-------------------------------------------------------- pl <- peaks(aa,10) peaksCount(aa,10) head(pl) plot(pl[,1], pl[,2], type="h", lwd=1) ## ----close the file------------------------------------------------------ close(aa) ## ----openid-------------------------------------------------------------- library(mzR) library(msdata) file <- system.file("mzid", "Tandem.mzid.gz", package="msdata") x <- openIDfile(file) ## ----metadata------------------------------------------------------------ mzidInfo(x) ## ----psms0--------------------------------------------------------------- p <- psms(x) colnames(p) ## ----psms1--------------------------------------------------------------- m <- modifications(x) head(m) ## ----psms2--------------------------------------------------------------- scr <- score(x) colnames(scr) ## ----label=sessioninfo, results='asis', echo=FALSE----------------------- toLatex(sessionInfo())