## ----style, echo = FALSE, results = 'asis', message=FALSE---------------- BiocStyle::markdown() ## ----env, echo=FALSE, message=FALSE, warning=FALSE----------------------- library("Pbase") ## ----pplot, echo=FALSE, fig.width=8.5, fig.height=8.5-------------------- Pbase:::pplot() ## ----fa, cache=TRUE------------------------------------------------------ library("Biostrings") fafile <- system.file("extdata/HUMAN_2015_02_selected.fasta", package = "Pbase") fa <- readAAStringSet(fafile) fa ## ----psm, cache=TRUE----------------------------------------------------- library("mzID") idfile <- system.file("extdata/Thermo_Hela_PRTC_selected.mzid", package = "Pbase") id <- flatten(mzID(idfile)) dim(id) head(id) ## ----p, cache=TRUE------------------------------------------------------- library("Pbase") p <- Proteins(fafile) p <- addIdentificationData(p, idfile) p ## ----paccess------------------------------------------------------------- aa(p) seqnames(p) pranges(p) pfeatures(p) ## ----metadata------------------------------------------------------------ metadata(p) acols(p) pcols(p) ## ----plot, fig.align='center', cache=TRUE-------------------------------- seqnames(p) plot(p[c(1,9)]) ## ----si------------------------------------------------------------------ sessionInfo()