https://github.com/lgatto/proteomicsannotationhubdata
Annotation hub data for proteomics data
https://github.com/lgatto/proteomicsannotationhubdata
Last synced: about 2 months ago
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Annotation hub data for proteomics data
- Host: GitHub
- URL: https://github.com/lgatto/proteomicsannotationhubdata
- Owner: lgatto
- Created: 2015-06-18T12:27:24.000Z (almost 10 years ago)
- Default Branch: master
- Last Pushed: 2022-01-06T11:46:42.000Z (over 3 years ago)
- Last Synced: 2025-01-20T23:12:50.246Z (3 months ago)
- Language: R
- Size: 106 KB
- Stars: 2
- Watchers: 4
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
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README
# `AnnotationHub` for proteomics
```{r env, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
suppressPackageStartupMessages(library("BiocStyle"))
```
The aim of this package is to offer access to mass spectrometry and
proteomics data throught the `r Biocpkg("AnnotationHub")`
infrastructure.
```{r ahinit}
library("AnnotationHub")
ah <- AnnotationHub()
ah
```
Let's start by querying the entries that originate from the PRIDE
database:
```{r provider}
query(ah, "PRIDE")
```
Or those of a specific project
```{r title}
ah[grep("PXD000001", ah$title)]
```
To see the metadata of a specific entry, we use its AnnotationHub
entry number inside single `[`
```{r ah49008}
ah["AH49008"]
```
To access the actual data, raw mass spectrometry data in this case, we
double the `[[`
```{r rawmsdata}
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.