R Markdown

This is an R Markdown document to show the steps for downloading proteomics data using R

#ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD024206/HepG2%20digests%20500ng%20SiO2NP%204h%202_1.tdf
if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
## Bioconductor version '3.15' is out-of-date; the current release version '3.16'
##   is available with R version '4.2'; see https://bioconductor.org/install
BiocManager::install("rpx")
## 'getOption("repos")' replaces Bioconductor standard repositories, see
## '?repositories' for details
## 
## replacement repositories:
##     CRAN: http://rspm/default/__linux__/focal/latest
## Bioconductor version 3.15 (BiocManager 1.30.19), R 4.2.2 (2022-10-31)
## Warning: package(s) not installed when version(s) same as or greater than current; use
##   `force = TRUE` to re-install: 'rpx'
## Installation paths not writeable, unable to update packages
##   path: /opt/R/4.2.2/lib/R/library
##   packages:
##     boot, class, codetools, foreign, MASS, Matrix, nlme, spatial, survival
library("rpx")

#Example with dataset on HeLa cells with different digest protocols
#881 files
id <- "PXD000900"
px <- PXDataset(id)
## Loading PXD000900 from cache.
pxfiles(px)
## Project PXD000900 files (881):
##  [local]  HeLa_ACE_CID_1.raw
##  [remote] HeLa_ACE_HCD_1.raw
##  [remote] HeLa_ACT_CID_1.raw
##  [remote] HeLa_ACT_HCD_1.raw
##  [remote] HeLa_AET_CID_1.raw
##  [remote] HeLa_AET_HCD_1.raw
##  [remote] HeLa_AGC_CID_1.raw
##  [remote] HeLa_AGC_HCD_1.raw
##  [remote] HeLa_AGE_CID_1.raw
##  [remote] HeLa_AGE_HCD_1.raw
##  ...
f <- pxget(px, "HeLa_ACE_CID_1.raw")
## Loading HeLa_ACE_CID_1.raw from cache.