In booker-tremayne/new-prideR: Explore the Pride Archive in R

knitr::opts_chunk$set(
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  fig.path = "man/figures/README-",
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library(newprideR)

Introduction

NewprideR allows for exploring the Pride archive through R. NewprideR has classes and functions for Pride projects, files, peptides, and proteins. It allows for most search functionality featured on the Pride Archive website, and a bit more. This makes systematically searching, and downloading possible solely in R.

All metadata received is obtained through the Pride Swagger UI API, which can be found here: https://www.ebi.ac.uk/pride/ws/archive/v2/swagger-ui.html

Installation

First install the package devtools if not installed already, then use install_github().

install.package("devtools")
library(devtools)
install_github("booker-tremayne/new-prideR")

Basic Use

Project Summaries

Project Summaries are how meta data for projects are stored.

search.ProjectSummary() is the function to search for projects across Pride. It can accept:

• keywords: will return projects that feature the given word within the entire metadata
• filters: which will only return projects that have a value in a given field
• page sorting: specifies how many projects per page, which page accessed, and whether it will sort by ascending or descending order.

For example:

project.list <- search.ProjectSummary(keywords = "imaging", page.size = 2, page.number = 4, instrument = "LTQ Orbitrap")
project.list

get.ProjectSummary() retrieves more detailed information regarding a single project. It accepts project accessions.

first.project <- get.ProjectSummary("PXD000001")
first.project

list.ProjectSummary() retrieves projects from newest to oldest, only accepting page size and page number. get.similar.projects() accepts a project accession and returns projects Pride deems similar.

File Details and File Detail Lists

File Details store metadata corresponding to files which projects contain.

File Detail Lists File Details and their associated project projects. It is intended for lists that contain multiple Project Summaries and their respective File Details

get.FileDetail() is used to get FileDetail data from a project. It accepts project accessions.

get.FileDetailList() gets all the FileDetails from a list of Project Summaries given to it.

search.FileDetail() is the searching function for File Details. It can accept:

• ProjectSummary list/FileDetailList Can be either object
• keywords : will return projects which contain files with the given keywords in their file name. Can be used to check file extensions.
• a file type : will return projects which contain files with the given file type. File types are categories given by Pride. They are as follows ; "RAW", "SEARCH", "RESULT", "PEAK", "FASTA", "SPECTRUM_LIBRARY", "GEL", "PARAMETERS_FILE", "OTHER"
• a file size range : will return projects which contain a file of the given size in bytes.
• all/any logic : specifies whether a project must contain files with file names of every keyword or a single keyword
• use.regex : specifies whether they keyword given is to be interpreted as a regular expression or exactly.

Note that this returns a list of FileDetailList objects.

For example:

project.list <- search.ProjectSummary(keywords = "imaging", page.size = 2, page.number = 19, instrument = "LTQ Orbitrap")
file.list <- search.FileDetail(project.list, keywords = c(".tif", ".ibd", ".imzml"), all = TRUE)
file.list

download.by.accession() downloads all files from a project, accepting a project accession string. download.project.list() downloads all files from all projects in a project list, accepting a list of Project Summaries. Names for folders are created according to the project title. download.by.name() downloads a single file according to the file name.

Note that get.FileDetailList() will be slow, and search.FileDetail() will take a few minutes if given a Project Summary list and not a FileDetailList.

Peptide Details

Peptide Details stores metadata for peptides within Pride.

get.PeptideDetail.accession() accepts an accession, and returns a list of peptides assocaited with the given project.

peptide.list <- get.PeptideDetail.accession("PXD019134", page.size = 2)
peptide.list

get.list.PeptideDetail() returns a list of all peptides from Pride, accepting page size and page number.

Protein Details

Protein Details stores metadata for proteins within Pride, and is similar to peptide details

get.ProteinDetail.accession() accepts an accession, and returns a list of peptides assocaited with the given project.

protein.list <- get.ProteinDetail.accession("PXD019134", page.size = 2)
protein.list

get.list.ProteinDetail() returns a list of all peptides from Pride, accepting page size and page number.

Example

We wish to obtain the projects that can be analyzed with Cardinal. For this, we need projects that contain ".ibd" and ."imzml" files. First, we should obtain all projects that contain the word "imaging" or "msi". This is necessary since the file searching method is slow when searching across several projects. We also wish for all the results to be focused on breast cancer.

imaging.list <- search.ProjectSummary(c("imaging", "msi"), page.size = 100, disease = "Breast cancer")

Now, we must retrieve only projects containing the file extensions ".imzml" and ".ibd".

successful.list <- search.FileDetail(imaging.list, c(".imzml", ".ibd"), all = TRUE)
successful.list

Finally, we want an optical image in our projects to analyze as well. To do so, we may search for projects containing files with the extension ".jpg" or ".jpeg" or ".tif" or ".png". We can feed our previous successful list into the search.project.list() function to do so.

final.list <- search.FileDetail(successful.list, c(".jpg", ".jpeg", ".tif", ".png"))
final.list

Now we may choose to download this/these projects.

download.project.list(final.list, "/users/UserName/exampleDownload")

booker-tremayne/new-prideR documentation built on Dec. 19, 2021, 10:48 a.m.