Introduction

The goal of the rpx package is to provide programmatic access to proteomics data from R, in particular to the ProteomeXchange (PX) central repository (see http://www.proteomexchange.org/ and http://central.proteomexchange.org/).

Vizcaino J.A. et al. ProteomeXchange: globally co-ordinated proteomics data submission and dissemination, Nature Biotechnology 2014, 32, 223 – 226, doi:10.1038/nbt.2839.

Additional repositories are likely to be added in the future.

The rpx package

PXDataset objects

The central object that handles data access is the PXDataset class. Such an instance can be generated by passing a valid PX experiment identifier to the PXDataset constructor.

library("rpx")
id <- "PXD000001"
px <- PXDataset(id)
px
## Object of class "PXDataset"
##  Id: PXD000001 with 11 files
##  [1] 'F063721.dat' ... [11] 'erwinia_carotovora.fasta'
##  Use 'pxfiles(.)' to see all files.

Data and meta-data

Several attributes can be extracted from an PXDataset instance, as described below.

The experiment identifier, that was originally used to create the PXDataset instance can be extracted with the pxid() method:

pxid(px)
## [1] "PXD000001"

The file transfer url where the data files can be accessed can be queried with the pxurl method:

pxurl(px)
## [1] "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001"

The species the data has been generated the data can be obtain calling the pxtax function:

pxtax(px)
## [1] "Erwinia carotovora"

Relevant bibliographic references can be queried with the pxref method:

strwrap(pxref(px))
## [1] "Gatto L, Christoforou A. Using R and Bioconductor for proteomics data"
## [2] "analysis. Biochim Biophys Acta. 2013 May 18. doi:pii:"                
## [3] "S1570-9639(13)00186-6. 10.1016/j.bbapap.2013.04.032"

All files available for the PX experiment can be obtained with the pxfiles method:

pxfiles(px)
##  [1] "F063721.dat"                                                         
##  [2] "F063721.dat-mztab.txt"                                               
##  [3] "PRIDE_Exp_Complete_Ac_22134.xml.gz"                                  
##  [4] "PRIDE_Exp_mzData_Ac_22134.xml.gz"                                    
##  [5] "PXD000001_mztab.txt"                                                 
##  [6] "README.txt"                                                          
##  [7] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML" 
##  [8] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzXML"
##  [9] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML"         
## [10] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw"           
## [11] "erwinia_carotovora.fasta"

The complete or partial data set can be downloaded with the pxget() function. The function takes an instance of class PXDataset as first mandatory argument.

The next argument, list, specifies what files to download. If missing, a menu is printed and the user can select a file. If set to "all", all files of the experiment are downloaded. Alternatively, numerics or logicals can also be used to subset the relevant files to be downloaded based on the pxfiles(.) output.

f <- pxget(px, "PXD000001_mztab.txt")
## Downloading PXD000001_mztab.txt file.
f
## [1] "/home/biocbuild/.cache/rpx/63ac7ca2511d_PXD000001_mztab.txt"

The rpx package makes use of the BiocFileCache package to avoid repeatedly dowloading files. When downloaded, file are cached, i.e. stored centrally in the package's cache directory. Next time the pxget() function attempts to get that file, it will be directly retrieved from the cache instead being downloaded again.

Finally, a list of recent PX additions and updates can be obtained using the pxannounced() function:

pxannounced()
## 15 new ProteomeXchange annoucements
##     Data.Set    Publication.Data Message
## 1  PXD018092 2021-01-15 13:33:58     New
## 2  PXD021074 2021-01-15 09:18:50     New
## 3  PXD019111 2021-01-15 08:23:52     New
## 4  PXD014134 2021-01-15 08:23:08     New
## 5  PXD007592 2021-01-15 08:17:11     New
## 6  PXD019079 2021-01-15 08:16:02     New
## 7  PXD017100 2021-01-14 15:00:06     New
## 8  PXD018559 2021-01-14 13:55:05     New
## 9  PXD023021 2021-01-14 12:26:15     New
## 10 PXD019111 2021-01-14 12:23:50     New
## 11 PXD013934 2021-01-14 12:22:16     New
## 12 PXD020669 2021-01-14 12:09:48     New
## 13 PXD020808 2021-01-14 08:47:49     New
## 14 PXD016881 2021-01-14 08:38:42     New
## 15 PXD022694 2021-01-14 08:35:49     New

A simple use-case

Below, we download the fasta file from the PXD000001 dataset and load it with the Biostrings package.

fas <- grep("fasta", pxfiles(px), value = TRUE)
fas
## [1] "erwinia_carotovora.fasta"
f <- pxget(px, fas)
## Downloading erwinia_carotovora.fasta file.
f ## files available in the rpx cache
## [1] "/home/biocbuild/.cache/rpx/63ac5832dd30_erwinia_carotovora.fasta"
library("Biostrings")
readAAStringSet(f)
## AAStringSet object of length 4499:
##        width seq                                            names               
##    [1]   147 MADITLISGSTLGSAEYVAEHL...QHQIPEDPAEEWLGSWVNLLK ECA0001 putative ...
##    [2]   153 VAEIYQIDNLDRGILSALMENA...EIQSTETLISLQNPIMRTIAP ECA0002 AsnC-fami...
##    [3]   330 MKKQYIEKQQQISFVKSFFSSQ...IGQVQCGVWPQPLRESVSGLL ECA0003 putative ...
##    [4]   492 MITLESLEMLLSIDENELLDDL...WRFDTGLKSRLMRRWQHGKAY ECA0004 conserved...
##    [5]   499 MRQTAALAERISRLSHALEHGL...AKIEASLQQVAEQIQQSEQQD ECA0005 conserved...
##    ...   ... ...
## [4495]   634 MSDKIIHLTDDSFDTDVLKADG...RRKVDPLRVFASDMARRLELL trx-rv3790 trx-rv...
## [4496]    93 MTKMNNKARRTARELKHLGASI...RELRDEFPMGYLGDYKDDDDK TimBlower TimBlower
## [4497]   309 MFSNLSKRWAQRTLSKSFYSTA...KFKWAGIKTRKFVFNPPKPRK sp|P07143|CY1_YEA...
## [4498]   231 FPTDDDDKIVGGYTCAANSIPY...PGVYTKVCNYVNWIQQTIAAN sp|P00761|TRYP_PI...
## [4499]   269 GVSGSCNIDVVCPEGNGHRDVI...DAAGTGAQFIDGLDSTGTPPV sp|Q7M135|LYSC_LY...

Questions and help

Either post questions on the Bioconductor support forum or open a GitHub issue.

Session information

sessionInfo()
## R version 4.0.3 (2020-10-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.5 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.12-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.12-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
## [1] rpx_1.26.1          Biostrings_2.58.0   XVector_0.30.0     
## [4] IRanges_2.24.1      S4Vectors_0.28.1    BiocGenerics_0.36.0
## [7] BiocStyle_2.18.1   
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.6           pillar_1.4.7         compiler_4.0.3      
##  [4] BiocManager_1.30.10  dbplyr_2.0.0         bitops_1.0-6        
##  [7] tools_4.0.3          zlibbioc_1.36.0      digest_0.6.27       
## [10] bit_4.0.4            BiocFileCache_1.14.0 RSQLite_2.2.2       
## [13] evaluate_0.14        memoise_1.1.0        lifecycle_0.2.0     
## [16] tibble_3.0.5         pkgconfig_2.0.3      rlang_0.4.10        
## [19] DBI_1.1.1            curl_4.3             yaml_2.2.1          
## [22] xfun_0.20            withr_2.3.0          httr_1.4.2          
## [25] stringr_1.4.0        dplyr_1.0.3          xml2_1.3.2          
## [28] knitr_1.30           rappdirs_0.3.1       generics_0.1.0      
## [31] vctrs_0.3.6          tidyselect_1.1.0     bit64_4.0.5         
## [34] glue_1.4.2           R6_2.5.0             rmarkdown_2.6       
## [37] purrr_0.3.4          blob_1.2.1           magrittr_2.0.1      
## [40] ellipsis_0.3.1       htmltools_0.5.1      assertthat_0.2.1    
## [43] stringi_1.5.3        RCurl_1.98-1.2       crayon_1.3.4