EnrichDO

EnrichDO is a double weighted iterative model by integrating the DO graph topology on a global scale. EnrichDO was based on the latest annotations of the human genome with DO terms, and double weighted the annotated genes. On one hand, to reinforce the saliency of direct gene-DO annotations, different initial weights were assigned to directly annotated genes and indirectly annotated genes, respectively. On the other hand, to detect locally most significant node between the parent and its children, less significant nodes were dynamically down-weighted. EnrichDO exhibits higher accuracy that often yield more specific significant DO terms, which alleviate the over enriched problem. EnrichDO input genes as NCBI Entrez ID format.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

##Release version
BiocManager::install("EnrichDO")


## Devel version
BiocManager::install(version='devel')
BiocManager::install("EnrichDO")

Example

After installation, check vignettes with:

browseVigenttes("EnrichDO")

Run cases are stored in inst/scripts/EnrichDO_exampleTest.R

The input data case is stored at inst/extdata/Alzheimer_curated.csv

Output example of enrichment result is available in inst/examples/result.txt

The thesis data is in thesisData folder (https://github.com/liangcheng-hrbmu/EnrichDO/thesisData/) and extdata_interpretation.txt explains the data source.