| Type: | Package |
| Title: | Retrieve Disease-Related Genes from Public Sources |
| Version: | 0.1.0 |
| Description: | For researchers to quickly and comprehensively acquire disease genes, so as to understand the mechanism of disease, we developed this program to acquire disease-related genes. The data is integrated from three public databases. The three databases are 'eDGAR', 'DrugBank' and 'MalaCards'. The 'eDGAR' is a comprehensive database, containing data on the relationship between disease and genes. 'DrugBank' contains information on 13443 drugs and 5157 targets. 'MalaCards' integrates human disease information, including disease-related genes. |
| Depends: | R (≥ 3.5.0) |
| LazyData: | TRUE |
| License: | GPL (≥ 3) |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.1.0 |
| NeedsCompilation: | no |
| Packaged: | 2020-04-24 06:34:09 UTC; tsl-wujiawei |
| Author: | Jiawei Wu [aut, cre], Xu Li [aut] |
| Maintainer: | Jiawei Wu <jared_wood@163.com> |
| Repository: | CRAN |
| Date/Publication: | 2020-04-24 09:40:02 UTC |
Get disease-related genes from eDGAR, DrugBank and MalaCards
Description
Get disease-related genes from eDGAR, DrugBank and MalaCards
Usage
AutoSeed(search)
Arguments
search |
Name of the disease |
Value
result$edgar: Containing Disease Name, OMIM ID and Genesymbol (Data comes from the eDGAR) result$malacards: Containing genes related to the disease (Data comes from the MalaCards) result$drugbank: Containing genes related to the disease (Data comes from the DrugBank)
Examples
result = AutoSeed("diabetes")
Relationship between gene and disease
Description
The data was collected in the drugbank. We got 27728 relationships between various disease and their related genes.
Usage
data("drugbank")Format
A data frame with 27728 observations on the following 2 variables.
Details
There are two columns in the data. The first column is genes and the second column is diseases.
Source
<https://www.drugbank.ca/>
Examples
data(drugbank)
Get disease-related genes from DrugBank.
Description
Get disease-related genes from DrugBank.
Usage
drugbank_disease_gene(search)
Arguments
search |
Name of the disease, character |
Value
The genes related to the disease, list
Examples
result = drugbank_disease_gene("diabetes")
Relationship between the gene and disease in edgar
Description
The function "edgar_disease_gene()" will generate the relationship between gene and disease depend on this dataset.
Usage
data("edgar")Format
A data frame with 1038340 observations on the following 2 variables.
Details
We got a total of 1038340 diseases and genes. There are two columns in the data. The first column is genes and the second column is diseases.
Source
<http://edgar.biocomp.unibo.it/gene_disease_db/>
Examples
data(edgar)
Get disease-related genes from eDGAR
Description
Get disease-related genes from eDGAR
Usage
edgar_disease_gene(disease)
Arguments
disease |
Name of the disease, character |
Value
a vector containing genesymbol related to the disease
Examples
result = edgar_disease_gene("diabetes")
The relationship between gene and disease
Description
The data was collected in the Malacards. We got 241306 relationships between various disease and their related genes.
Usage
data("mala")Format
A data frame with 241306 observations on the following 2 variables.
Details
We got a total of 241306 diseases and genes. There are two columns in the data. The first column is disease and the second column is gene.
Source
<https://doi.org/10.1093/nar/gkw1012>
Examples
data(mala)
Get disease-related genes from MalaCards
Description
Get disease-related genes from MalaCards
Usage
malacards_disease_gene(disease)
Arguments
disease |
Name of the disease |
Value
The genes related to the disease, character vector
Examples
result = malacards_disease_gene("diabetes")