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https://github.com/omicsdi/ddir
An R package to access to Omics Discovery Index API
https://github.com/omicsdi/ddir
multiomics omicsdi r rest-client
Last synced: 11 days ago
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An R package to access to Omics Discovery Index API
- Host: GitHub
- URL: https://github.com/omicsdi/ddir
- Owner: OmicsDI
- License: apache-2.0
- Created: 2015-11-01T09:55:46.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2020-03-30T16:18:10.000Z (over 4 years ago)
- Last Synced: 2024-03-26T05:51:22.113Z (9 months ago)
- Topics: multiomics, omicsdi, r, rest-client
- Language: R
- Size: 294 MB
- Stars: 2
- Watchers: 6
- Forks: 5
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://travis-ci.org/enriquea/ddiR)
[ddiR](https://github.com/BD2K-DDI/ddiR)
======
An [R package](https://github.com/BD2K-DDI/ddiR) to obtain data from the Omics Discovery Index ([OmicsDI](http://www.omicsdi.org). It uses its RESTful Web Services at [OmicsDI WS](http://www.omicsdi.org/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
```R
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
```R
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
```R
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
```R
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
```R
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.
```R
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 = [email protected], database = dataset@database)
rank = 0
for(similarDataset in Similar@datasets){
print(paste([email protected], [email protected], similarDataset@score, [email protected], rank))
rank = rank + 1
}
}
}
sink()
```
### Maintainers
[Yasset Perez-Riverol](https://github.com/ypriverol)
[Ariana Barbera Betancourt](http://github.com/abb44)
[Enrique Audain](https://github.com/enriquea)