## ----env, echo = FALSE--------------------------------------------------- suppressPackageStartupMessages(library("BiocStyle")) 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-------------------------------------------------------------- (i <- grep("fasta", pxfiles(px))) pxget(px, i) ## 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", version = "0.9")) head(exprs(x)) head(fData(x)[, 1:2]) ## ----si------------------------------------------------------------------ sessionInfo() ## ----clean, echo = FALSE------------------------------------------------- unlink("erwinia_carotovora.fasta") unlink("F063721.dat-mztab.txt")