ddir's Introduction

ddiR

An R package to obtain data from the Omics Discovery Index (OmicsDI. It uses its RESTful Web Services at OmicsDI WS for that purpose.

Currently, the following domain entities are supported:

Dataset as S4 objects, including methods to get them from OmicsDI by accession and as.data.frame
Publication as S4 objects, including methods to get them from OmicsDI by accession and as.data.frame
Term as S4 objects, including methods to get them from OmicsDI by term and as.data.frame

Installation

First, we need to install devtools:

install.packages("devtools")
library(devtools)

Then we just call

install_github("enriquea/ddiR")
library(ddiR)

Examples

This example retrives all dataset details given accession and database identifier

library(ddiR)

dataset = get.DatasetDetail(accession="PXD000210", database="pride")

# print dataset full name
get.dataset.name(dataset)

# print dataset omics type
get.dataset.omics(dataset)

Access to all datasets for NOTCH1 gene

datasets <- search.DatasetsSummary(query = "NOTCH1")

sink("outfile.txt")
for(datasetCount in seq(from = 0, to = datasets@count, by = 100)){

    datasets <- search.DatasetsSummary(query = "NOTCH1", start = datasetCount, size = 100)

    for(dataset in datasets@datasets){
             dataset = get.DatasetDetail(accession=dataset.id(dataset), database=database(dataset))
             print(paste(dataset.id(dataset), get.dataset.omics(dataset), get.dataset.link(dataset)))
            }
    }
}
sink()

Getting the dataset IDs and full link of 20 Genomics studies in Cancer

datasets <- search.DatasetsSummary(query = "Cancer AND Genomics")

for(dataset in datasets@datasets){
    dataset = get.DatasetDetail(accession=dataset.id(dataset), database=database(dataset))
    print(paste(dataset.id(dataset), get.dataset.link(dataset), sep = ' '))
}

Print the dataset IDs and short description of 20 Proteomics studies for tumor supressor p53

datasets <- search.DatasetsSummary(query = "p53 AND Proteomics")

for(dataset in datasets@datasets){
    dataset = get.DatasetDetail(accession=dataset.id(dataset), database=database(dataset))
    print(paste(dataset.id(dataset), get.dataset.name(dataset), sep = ' '))
}

Getting Proteomics studies in Heart tissue from PRIDE database

datasets <- search.DatasetsSummary(query = "Heart")

for(dataset in datasets@datasets){
    dataset = get.DatasetDetail(accession=dataset.id(dataset), database=database(dataset))
    if(database(dataset)=='pride')
    print(paste(dataset.id(dataset), get.dataset.tissues(dataset), get.dataset.omics(dataset), sep = ' '))
}

This exmaple shows how retrieve all the metadata similarity scores by using the R-package ddiR.

datasets <- search.DatasetsSummary(query = "*:*")
i  = 0
sink("outfile.txt")
for(datasetCount in seq(from = 0, to = datasets@count, by = 100)){

    datasets <- search.DatasetsSummary(query = "*:*", start = datasetCount, size = 100)

    for(dataset in datasets@datasets){
            Similar = get.MetadataSimilars(accession = dataset@dataset.id, database = dataset@database)
            rank = 0
            for(similarDataset in Similar@datasets){
                print(paste(dataset@dataset.id, similarDataset@dataset.id, similarDataset@score, dataset@omics.type, rank))
                rank = rank + 1
            }
    }
}
sink()

Maintainers

Yasset Perez-Riverol
Ariana Barbera Betancourt
Enrique Audain

ddir's People

Contributors

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ddir's Issues

Some examples from the python library

Please, Enrique try to implement also these examples in the R package as we are trying to implement in the python package OmicsDI/ddipy#1

Error during installing ddiR

I am getting this error during installation of ddiR package. Please check the log pasted below.

>install_github("BD2K-DDI/ddiR")
Downloading GitHub repo BD2K-DDI/ddiR@master
√  checking for file 'C:\Users\anura\AppData\Local\Temp\Rtmpay05qJ\remotes1d385ecc7adb\OmicsDI-ddiR-e672b59/DESCRIPTION' ...
-  preparing 'ddiR': (2.2s)
√  checking DESCRIPTION meta-information ...
   Warning: C:/Users/anura/AppData/Local/Temp/RtmpAR3sba/Rbuild36603bd502d/ddiR/man/get.MetadataSimilars.Rd:23: unexpected section header '\name'
   Warning: C:/Users/anura/AppData/Local/Temp/RtmpAR3sba/Rbuild36603bd502d/ddiR/man/get.MetadataSimilars.Rd:24: unexpected section header '\alias'
   Warning: C:/Users/anura/AppData/Local/Temp/RtmpAR3sba/Rbuild36603bd502d/ddiR/man/get.MetadataSimilars.Rd:25: unexpected section header '\title'
   Warning: C:/Users/anura/AppData/Local/Temp/RtmpAR3sba/Rbuild36603bd502d/ddiR/man/get.MetadataSimilars.Rd:27: unexpected section header '\usage'
   Warning: C:/Users/anura/AppData/Local/Temp/RtmpAR3sba/Rbuild36603bd502d/ddiR/man/get.MetadataSimilars.Rd:30: unexpected section header '\arguments'
   Warning: C:/Users/anura/AppData/Local/Temp/RtmpAR3sba/Rbuild36603bd502d/ddiR/man/get.MetadataSimilars.Rd:31: unknown macro '\item'
   Warning: C:/Users/anura/AppData/Local/Temp/RtmpAR3sba/Rbuild36603bd502d/ddiR/man/get.MetadataSimilars.Rd:33: unknown macro '\item'
   Warning: C:/Users/anura/AppData/Local/Temp/RtmpAR3sba/Rbuild36603bd502d/ddiR/man/get.MetadataSimilars.Rd:35: unexpected section header '\value'
   Warning: C:/Users/anura/AppData/Local/Temp/RtmpAR3sba/Rbuild36603bd502d/ddiR/man/get.MetadataSimilars.Rd:38: unexpected section header '\description'
   Warning: C:/Users/anura/AppData/Local/Temp/RtmpAR3sba/Rbuild36603bd502d/ddiR/man/get.MetadataSimilars.Rd:42: unexpected section header '\author'
   Warning: C:/Users/anura/AppData/Local/Temp/RtmpAR3sba/Rbuild36603bd502d/ddiR/man/get.MetadataSimilars.Rd:47: unexpected END_OF_INPUT '
   '
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
-  building 'ddiR_0.99.0.tar.gz'
   
Installing package into ‘C:/Users/anura/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
* installing *source* package 'ddiR' ...
** R
Error in parse(outFile) : 
  C:/Users/anura/AppData/Local/Temp/RtmpstQdLP/R.INSTALL4ac63a914b8/ddiR/R/AllClasses.R:80:1: unexpected input
79:       visit.count = "numeric",
80: <<
    ^
ERROR: unable to collate and parse R files for package 'ddiR'
* removing 'C:/Users/anura/Documents/R/win-library/3.5/ddiR'
In R CMD INSTALL
Error in i.p(...) : 
  (converted from warning) installation of package ‘C:/Users/anura/AppData/Local/Temp/Rtmpay05qJ/file1d3862a81ab/ddiR_0.99.0.tar.gz’ had non-zero exit status

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