## ----env, echo = FALSE-------------------------------------------------------- suppressPackageStartupMessages(library("BiocStyle")) suppressPackageStartupMessages(library("Biostrings")) ## ----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-------------------------------------------------------------------- f <- pxget(px, "F063721.dat-mztab.txt") f ## ----more, warning=FALSE------------------------------------------------------ fas <- grep("fasta", pxfiles(px), value = TRUE) fas f <- pxget(px, fas) ## file available in the rpx cache f ## ----example1, message = FALSE------------------------------------------------ library("Biostrings") readAAStringSet(f) ## ----si----------------------------------------------------------------------- sessionInfo()