## ----style, eval=TRUE, echo=FALSE, results='asis'------------------------
BiocStyle::latex()


## ----env, echo=FALSE-----------------------------------------------------
suppressPackageStartupMessages(library("Biostrings"))
suppressPackageStartupMessages(library("MSnbase"))


## ----pxdata--------------------------------------------------------------
library("rpx")
id <- "PXD000001"
px <- PXDataset(id)
px


## ----pxid----------------------------------------------------------------
pxid(px)


## ----purl----------------------------------------------------------------
pxurl(px)


## ----pxtax---------------------------------------------------------------
pxtax(px)


## ----pxref---------------------------------------------------------------
strwrap(pxref(px))


## ----pxfiles-------------------------------------------------------------
pxfiles(px)


## ----pxget---------------------------------------------------------------
pxget(px, "erwinia_carotovora.fasta")
dir(pattern = "fasta")


## ----pxget2--------------------------------------------------------------
pxget(px, 8) ## same as above


## ----pxan----------------------------------------------------------------
pxannounced()


## ----more, warning=FALSE-------------------------------------------------
(mzt <- grep("F0.+mztab", pxfiles(px), value = TRUE))
(fas <- grep("fasta", pxfiles(px), value = TRUE))
pxget(px, c(mzt, fas))

library("Biostrings")
readAAStringSet(fas)

library("MSnbase")
(x <- readMzTabData(mzt, "PEP"))
head(exprs(x))
head(fData(x)[, 1:2])


## ----sessioninfo, results='asis', echo=FALSE-----------------------------
toLatex(sessionInfo(), locale = FALSE)