In lgatto/ProteomicsAnnotationHubData: Transform public proteomics data resources into Bioconductor Data Structures

AnnotationHub for proteomics

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
suppressPackageStartupMessages(library("BiocStyle"))

The aim of this package is to offer access to mass spectrometry and proteomics data throught the r Biocpkg("AnnotationHub") infrastructure.

library("AnnotationHub")
ah <- AnnotationHub()
ah

Let's start by querying the entries that originate from the PRIDE database:

query(ah, "PRIDE")

Or those of a specific project

ah[grep("PXD000001", ah$title)]

To see the metadata of a specific entry, we use its AnnotationHub entry number inside single [

ah["AH49008"]

To access the actual data, raw mass spectrometry data in this case, we double the [[

library("mzR")
rw <- ah[["AH49008"]]
rw

In this case, we have an instance of class r as.character(class(rw)), that can be processed as anticipated.

In the short demonstration above, we had direct and standardised access to the raw data, without a need to manually open this raw data or worry about the file format. The data was prepared and converted into a standard Bioconductor data types for immediate consumption by the user. This is also valid for other relevant data types such as identification results, fasta files or protein of peptide quantitation data.

See the ProteomicsAnnotationHubData vignette for details on available data and how to add new proteomics data to AnnotationHub.

lgatto/ProteomicsAnnotationHubData documentation built on Jan. 11, 2022, 3:41 a.m.